GREMLIN Database
Structures
Note: we are still working on uploading all the data and notes to our interactive website. In the meantime all the models can be accessed in the links below:
  • Starting models - Starting models for the iterative hybrid protocol. Based on the prefix you can determine where the models are coming from. (ab_v01) top10 denovo models using sigmoid only restraints. (ab_v02) top10 denovo models using bounded+sigmoid restraints during centroid, and sigmoid only during full atom stage. (mp) top10 map-align models from one round of hybrid.
  • Initial models - Top models from initial experiments where only the (ab_v01+ab_v02) OR mp models are iteratively hybridized
  • Top 30 models - Top 30 models across 30 iterations of hybrid of ab_v01+ab_v02 + map-align models.
  • Final models - Single model for each target.
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Page Title Function Type CON
A5D257 COB - PF01955 - CbiZ - Adenosylcobinamide amidohydrolase known SOL 08
P36561 COB - PF02654 - CobS Cobalamin-5-phosphate synthase (COBS_ECOLI) known MEM 09
Q05600 COB - PF03186 - CobD - Cobalamin biosynthesis protein CbiB known MEM 09
P29934 COB - PF06213 - CobT Cobalamin biosynthesis protein known SOL 09
F2J3R1 DUF - PF09956 - DUF2190 unknown SOL 07
A1B6L5 DUF - PF10983 - DUF2793 (NEW FOLD) unknown SOL 08
W8F819 DUF - PF11138 - DUF2911 (NEW FOLD) unknown SOL 09
P43329 DUF - PF11898 - DUF3418 - (C-term of ATP-dependent RNA helicase HrpA) unknown SOL 08
K4LFA1 DUF - PF12654 - DUF3786 (NEW FOLD) unknown SOL 09
U2SXM1 DUF - PF12957 - DUF3846 (NEW FOLD) unknown SOL 07
Q8A843 DUF - PF14902 - DUF4494 (NEW FOLD) unknown SOL 07
K9RI92 IMM - PF15562 - Immunity protein 17 known MEM 09
P54463 PF02690 - NaPi-cotransporter (YQEW_BACSU) known MEM 09
A0YGE7 PF03203 - MerC mercury resistance protein known SOL 08
P42601 PF03741 - Integral membrane protein TerC family (ALX_ECOLI) known MEM 08
P27620 PF03808 - Glycosyl transferase WecB_TagA_CpsF family (TAGA_BACSU) known SOL 09
A1K5M7 PF04168 - A predicted alpha-helical domain with a conserved ER motif. known SOL 08
D2NPP5 PF04213 - DNA-directed RNA polymerase, beta subunit (Htaa) known SOL 07
E6SL09 PF04308 - Ribonuclease H-like known SOL 08
P76506 PF04333 - phospholipid-binding lipoprotein MlaA (MLAA_ECOLI) known SOL 07
P38097 PF05231 - MASE1 - diguanylate cyclase (YEGE_ECOLI) known MEM 08
B5H6C0 PF05800 - Gas vesicle synthesis protein known SOL 08
P25476 PF05944 - Phage small terminase subunit known SOL 09
G4QGG7 PF07452 - CHRD protein known SOL 08
P33650 PF07664 - Ferrous iron transport protein B (FEOB_ECOLI) known MEM 06
G4SYW9 PF08889 - WbqC-like protein family known SOL 08
P64578 PF09907 - mRNA interferase HigB (HIGB_ECOLI) known SOL 09
F2NGG5 PF10133 - RNA-binding protein known SOL 10
P0AE95 PF10627 - Curli assembly protein CsgE (CSGE_ECOLI) known SOL 08
A3SJX8 PF11836 - Phage tail tube protein, GTA-gp10 known SOL 08
G8MBE3 PF12531 - DNA-K related protein known SOL 08
B5YHG0 PF12637 - TSCPD domain known SOL 08
A0M6E0 PF14109 - Gliding motility lipoprotein GldH homolog known SOL 08
P13057 PF14350 - Beta protein known SOL 08
K0NPI0 PF14452 - Multiubiquitin known SOL 09
C7R645 PF14462 - Prokaryotic E2 family E known SOL 08
B8FBD4 PF16949 - Putative ATP-binding cassette known SOL 07
R6LGR9 SPORE - PF01944 - Stage II sporulation protein M known MEM 08
P49939 SPORE - PF03323 - Spore germination protein KA (GERKA_BACSU) known BOTH 08
P13801 SPORE - PF03419 - Sporulation sigma-E factor-processing peptidase (SP2G_BACSU) known BOTH 08
P49782 SPORE - PF09546 - Stage III sporulation protein AE (SP3AE_BACSU) known MEM 09
Q01368 SPORE - PF09548 - Stage III sporulation protein AB (SP3AB_BACSU) known BOTH 09
P39151 SPORE - PF09551 - Stage II sporulation protein R (SP2R_BACSU) known SOL 08
O32131 SPORE - PF09560 - Sporulation protein YunB (YUNB_BACSU) known SOL 07
D9RZD9 SPORE - PF12673 - Spore coat assembly protein SafA (NEW FOLD) known SOL 06
confident
Page Title Function Type CON
P0A6G5 CIT - PF03802 - Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase (CITX_ECOLI) known SOL 09
P69330 CIT - PF06857 - Malonate decarboxylase delta subunit (MdcD) (CITD_ECOLI) known SOL 08
P37908 DUF - PF01595 - DUF21 (YFJD_ECOLI) unknown MEM 09
P0AB28 DUF - PF02620 - DUF177 (YCED_ECOLI) unknown SOL 07
P55425 DUF - PF05284 - DUF736 unknown SOL 07
K0WKJ4 DUF - PF05359 - DUF748 unknown SOL 07
P76076 DUF - PF07027 - DUF1318 (YDBL_ECOLI) unknown SOL 09
Q98M99 DUF - PF07370 - DUF1489 unknown SOL 07
W8RPW9 DUF - PF07799 - DUF1643 unknown SOL 07
A2SCK5 DUF - PF08895 - DUF1840 unknown SOL 08
Q0KCJ0 DUF - PF08897 - DUF1841 unknown SOL 07
F2IAU5 DUF - PF09345 - DUF1987 unknown SOL 09
P50830 DUF - PF09369 - DUF1998 (YPRA_BACSU) known SOL 07
P51024 DUF - PF09831 - DUF2058 (YAIL_ECOLI) unknown SOL 07
Q8KCS8 DUF - PF09912 - DUF2141 unknown SOL 08
P96595 DUF - PF09954 - DUF2188 (YDAT_BACSU) unknown SOL 10
P39588 DUF - PF09962 - DUF2196 unknown SOL 08
B9L549 DUF - PF09969 - DUF2203 unknown BOTH 08
B2U851 DUF - PF09980 - DUF2214 unknown MEM 08
B6JCJ1 DUF - PF10003 - DUF2244 unknown BOTH 07
A5ERF9 DUF - PF10073 - DUF2312 unknown SOL 09
E6XBS6 DUF - PF10652 - DUF2480 unknown SOL 08
P9WKP4 DUF - PF10944 - DUF2630 unknown SOL 09
C3MA27 DUF - PF11003 - Protein of unknown function (DUF2842) unknown MEM 10
P44203 DUF - PF11008 - DUF2846 unknown SOL 09
Q2IJU1 DUF - PF11236 - DUF3037 unknown SOL 07
U5WRG4 DUF - PF11259 - DUF3060 unknown SOL 09
C1CZL3 DUF - PF11303 - DUF3105 unknown SOL 07
Q8YV69 DUF - PF11322 - DUF3124 unknown SOL 07
S6AIS6 DUF - PF11743 - DUF3301 unknown SOL 08
Q0AB14 DUF - PF11902 - DUF3422 unknown SOL 07
K0I3E1 DUF - PF11911 - DUF3429 unknown MEM 09
A0JVG1 DUF - PF12502 - DUF3710 unknown SOL 08
W8KWE5 DUF - PF12686 - DUF3800 (3-deoxy-D-manno-octulosonic acid transferase) unknown SOL 07
D3SEL0 DUF - PF13767 - Domain of unknown function (DUF4168) unknown SOL 10
W0RMX1 DUF - PF13858 - DUF4199 unknown MEM 09
A4YVY8 DUF - PF14081 - DUF4262 unknown SOL 08
E8MXR4 DUF - PF14088 - DUF4268 unknown SOL 08
Q8A2Y9 DUF - PF14127 - DUF4294 unknown SOL 09
W5TPN4 DUF - PF14155 - DUF4307 unknown SOL 08
I0HLM1 DUF - PF14235 - DUF4337 unknown MEM 10
D5MM10 DUF - PF14238 - DUF4340 unknown SOL 07
V5RWV1 DUF - PF14242 - DUF4342 unknown SOL 09
D5XAK5 DUF - PF14276 - DUF4363 unknown MEM 10
H1Y1B3 DUF - PF16117 - DUF4833 (NEW FOLD) unknown SOL 06
P9WKN6 DUF - PF16170 - DUF4873 unknown SOL 07
B2IUZ8 DUF - PF16277 - DUF4926 unknown SOL 09
B2TKH6 IMM - PF14112 - Immunity protein 22 known SOL 07
P46857 IMM - PF15567 - Immunity protein 35 (YRHB_ECOLI) known SOL 07
H3SK11 IMM - PF15580 - Immunity protein 53 known SOL 07
G7EKA3 IMM - PF15590 - Immunity protein 27 known SOL 07
F2JRC2 IMM - PF15595 - Immunity protein 51 known SOL 08
I4B5W3 IMM - PF15599 - Immunity protein 63 known SOL 08
A5FGG2 IMM - PF15631 - NTF2 fold immunity protein (lipoprotein) known SOL 08
P33135 PF01311 - Flagellar biosynthetic protein FliR (FLIR_ECOLI) known MEM 07
P0AC07 PF01313 - Flagellar biosynthetic protein FliQ (FLIQ_ECOLI) known MEM 08
P48190 PF01348 - Type II intron maturase (MATK_MAIZE) known SOL 09
Q06126 PF01610 - Transposase for insertion sequence element IS1001 known SOL 08
O34601 PF01809 - Putative membrane protein insertion efficiency factor known BOTH 08
P64564 PF02325 - YGGT family (YGGT_ECOLI) known MEM 09
Q7AKN0 PF02467 - Transcription factor WhiB known SOL 08
P64604 PF02470 MlaD protein (MLAD_ECOLI) known SOL 08
Q97UR7 PF02538 - Hydantoinase Boxoprolinase (Q97UR7_SULSO) known SOL 08
P54163 PF02592 - Putative vitamin uptake transporter (YPDP_BACSU) known MEM 08
P84624 PF02662 - F420-non-reducing hydrogenase iron-sulfur subunit D known SOL 09
P0ADC3 PF02687 - Lipoprotein-releasing system transmembrane protein - (LOLC_ECOLI) known BOTH 08
O05227 PF03334 - Na()H() antiporter subunit G known MEM 10
B8DKR2 PF03626 - Prokaryotic Cytochrome C oxidase subunit IV known MEM 08
P0ABX8 PF03748 - Flagellar protein FliL known SOL 08
O34318 PF03780 - Asp23 family, cell envelope-related function (YLOU_BACSU) known SOL 08
Q96G23 PF03798 - TLC domain (CERS2_HUMAN) known SOL 09
Q9HT13 PF03899 - ATP synthase I chain known MEM 09
Q47319 PF03942 - DTW domain-containing protein YfiP unknown SOL 08
A7INK9 PF03981 - Ubiquinol-cytochrome C chaperone known SOL 09
C5A8X2 PF04020 - Mycobacterial 4 TMS phage holin, superfamily IV known SOL 09
O31821 PF04138 - GtrA-like protein (YNGA_BACSU) known MEM 09
P0A710 PF04279 - Intracellular septation protein A (YCIB_ECOLI) known MEM 08
Q6Y1H2 PF04387 - Protein tyrosine phosphatase-like protein, PTPLA (HACD2_HUMAN) known SOL 07
Q98544 PF04947 - Putative transcription factor A494R known SOL 07
P27650 PF04955 - Protein HupE known MEM 09
P0AAP1 PF05230 - MASE2 domain (ADRA_ECOLI) known MEM 09
P08322 PF05309 - TraE protein (TRAE1_ECOLI) known SOL 09
O96011 PF05648 - Peroxisomal biogenesis factor 11 (PX11B_HUMAN) known MEM 07
P50359 PF05717 - TnpB_IS66 (y4hO) known SOL 06
O31469 PF06271 - RDD family (YCZC_BACSU) known BOTH 08
R6BJC6 PF06695 - Putative small multi-drug export protein known MEM 09
O30387 PF06750 - Bacterial Peptidase A24 N-terminal domain known MEM 09
Q3SW25 PF06793 - UPF0262 protein Nwi_0248 unknown SOL 07
Q56460 PF07291 - Methylamine utilisation protein MauE known MEM 08
Q89HG4 PF07483 - Bll6027 protein known SOL 09
Q1ITH1 PF07593 - ASPIC UnbV known SOL 09
D0LZC1 PF08495 - PF10442 - FIST known SOL 08
L0I8M6 PF08663 - HalX domain known SOL 09
E0ULT2 PF08707 - Primase 2 known SOL 09
A1WAS1 PF08859 - DGC domain known SOL 08
G8X4D5 PF09357 - RteC protein known SOL 07
Q74GB0 PF09527 - Putative F0F1-ATPase subunit Ca2Mg2 transporter known MEM 09
P25149 PF09529 - Integral membrane protein (YWAF_BACSU) unknown MEM 08
C3K8U5 PF09650 - Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn) known SOL 10
P9WM62 PF09678 - Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG) known MEM 08
Q02BV2 PF09721 - Transmembrane exosortase (Exosortase_EpsH) known MEM 08
O34738 PF09819 - ABC-type cobalt transport system, permease component (YKOE_BACSU) known MEM 09
W0REN7 PF09828 - Chromate resistance exported protein known SOL 08
E7DNB6 PF10145 - Phage-related minor tail protein (Tape measure protein) unknown SOL 09
I7IW01 PF10552 - ORF6C domain known SOL 09
F3Z2T5 PF10618 - Phage tail tube protein known SOL 06
E4TUT2 PF11335 - Galanin known SOL 06
Q20XH1 PF11390 - NADH-dependant formate dehydrogenase delta subunit FdsD known SOL 09
Q1QIT9 PF11749 - Molybdopterin-guanine dinucleotide biosynthesis protein A known SOL 06
P05684 PF11800 - Replication protein C C-terminal region known SOL 09
I3YD59 PF11812 - Phosphate ABC transporter membrane protein 2, PhoT family known BOTH 07
P0DJ98 PF12733 - Cadherin-like beta sandwich domain known SOL 08
P0AD40 PF12843 - Putative quorum-sensing-regulated virulence factor (YPEB_ECOLI) known SOL 09
E3JDH4 PF13376 - Bacteriocin-protection, YdeI or OmpD-Associated known SOL 08
A6GYP8 PF13562 - Probable sugar phosphate nucleotydyl transferase known SOL 07
Q1H1D1 PF13781 - DoxX-like family known MEM 09
P28916 PF13808 - H repeat-associated protein YbfD known SOL 09
Q96DM1 PF13843 - Transposase IS4 - PiggyBac transposable element-derived protein 4 (PGBD4_HUMAN) known SOL 07
G2NPC7 PF14030 - Putative secreted protein unknown SOL 07
W2CN18 PF14058 - PcfK-like protein known SOL 09
Q9K8V9 PF14168 - YjzC-like protein known SOL 07
R6MUZ6 PF14198 - Transposon-encoded protein TnpV known SOL 09
P46909 PF14256 - YwiC-like protein known MEM 08
A4T0M3 PF14334 - Putative periplasmic ligand-binding sensor protein unknown SOL 08
C0CV72 PF16079 - Phage holin family Hol44, in holin superfamily V known SOL 08
Q1QQ50 PF16998 - 17 kDa outer membrane surface antigen known SOL 07
P39072 SPORE - PF10646 - Sporulation and spore germination (GERM_BACSU) known SOL 08
refine
Page Title Function Type CON
Q57756 DUF - PF02596 - DUF169 unknown SOL 07
D5EBZ5 DUF - PF04034 - DUF367 (Probable ribosome biogenesis protein Mmah_1192) unknown SOL 07
W0RSF6 DUF - PF06718 - DUF1203 unknown SOL 07
Q7VXL2 DUF - PF08909 - DUF1854 unknown SOL 06
L0DAE5 DUF - PF10057 - DUF2294 unknown SOL 08
V6F740 DUF - PF11149 - DUF2924 unknown SOL 06
O31833 DUF - PF11188 - DUF2975 unknown MEM 08
D5UMZ9 DUF - PF11292 - DUF3093 unknown SOL 06
E4RXG7 DUF - PF11827 - DUF3347 unknown SOL 08
A6T7A7 DUF - PF12098 - DUF3574 (Choline dehydrogenase) unknown SOL 06
A7HPW4 DUF - PF12599 - DUF3768 unknown SOL 06
G2PQZ5 DUF - PF14060 - DUF4252 unknown SOL 06
P0AC05 PF00813 - Flagellar biosynthetic protein FliP (FLIP_ECOLI) known MEM 07
Q7WY60 PF01899 - Na_H antiporter subunit E (MRPE_BACSU) known BOTH 07
Q7Y4W4 PF03420 - Gp21 prohead core scaffold protein and protease known SOL 06
Q58990 PF03706 - Lysylphosphatidylglycerol synthase TM region known MEM 07
P42107 PF04235 - Protein of unknown function (DUF418) (YXAH_BACSU) unknown MEM 07
P46187 PF04246 - Protein RseC known BOTH 06
P0A905 PF05433 - Outer membrane lipoprotein SlyB known SOL 05
D2QZM7 PF05947 - Type VI secretion system, ImpG, VasA, VC_A0110 known SOL 07
G2IIW6 PF07879 - Polyhydroxyalkanoate synthesis repressor PhaR known SOL 07
R5U9B8 PF08800 - VirE N-terminal domain known SOL 08
Q2SNL6 PF14345 - GDYXXLXY unknown SOL 05
P71056 PF14897 - EpsG family (EPSG_BACSU) known MEM 07
A5A630 PF17090 - Uncharacterised protein family (YTCA_ECOLI) known MEM 09
O31625 SPORE - PF14069 - Stage VI sporulation protein F (SPVIF_BACSU) known SOL 08
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