Query psy8137
Match_columns 88
No_of_seqs 115 out of 526
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 19:30:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8137.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8137hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02020 W2: eIF4-gamma/eIF5/e 99.9 5E-28 1.1E-32 150.4 6.9 80 6-85 3-84 (84)
2 smart00515 eIF5C Domain at the 99.9 4.6E-24 1E-28 131.9 7.2 72 5-77 12-83 (83)
3 KOG2297|consensus 99.8 7.2E-19 1.6E-23 132.3 6.6 79 3-82 334-412 (412)
4 KOG2767|consensus 99.7 1.1E-17 2.3E-22 126.6 6.8 83 5-87 313-399 (400)
5 KOG1461|consensus 99.7 7.2E-17 1.6E-21 128.9 7.3 80 6-85 594-673 (673)
6 PF09851 SHOCT: Short C-termin 70.9 5.9 0.00013 19.9 2.4 19 29-47 5-23 (31)
7 PF00123 Hormone_2: Peptide ho 68.0 5.3 0.00011 19.9 1.8 12 64-75 16-27 (28)
8 smart00070 GLUCA Glucagon like 60.8 8.1 0.00018 19.1 1.7 12 64-75 16-27 (27)
9 smart00544 MA3 Domain in DAP-5 58.6 38 0.00082 20.8 5.0 48 5-52 32-80 (113)
10 PF03271 EB1: EB1-like C-termi 52.2 36 0.00078 18.4 3.6 28 10-37 12-43 (43)
11 smart00437 TOP1Ac Bacterial DN 47.7 29 0.00063 25.3 3.6 33 10-42 14-47 (259)
12 PF09090 MIF4G_like_2: MIF4G l 45.5 43 0.00093 24.2 4.1 45 6-53 92-136 (253)
13 cd08330 CARD_ASC_NALP1 Caspase 44.3 71 0.0015 19.3 4.6 47 27-77 16-73 (82)
14 cd00186 TOP1Ac DNA Topoisomera 41.7 38 0.00082 26.0 3.5 33 10-42 88-121 (381)
15 PF02847 MA3: MA3 domain; Int 37.6 56 0.0012 20.0 3.3 45 6-50 33-78 (113)
16 PF03801 Ndc80_HEC: HEC/Ndc80p 37.1 90 0.002 21.1 4.5 32 7-38 38-82 (157)
17 cd08329 CARD_BIRC2_BIRC3 Caspa 35.1 1.1E+02 0.0024 18.9 4.3 48 28-77 25-81 (94)
18 KOG3021|consensus 34.1 53 0.0012 24.8 3.1 19 2-20 270-288 (313)
19 PRK11001 mtlR mannitol repress 33.8 74 0.0016 22.3 3.6 34 12-46 49-82 (171)
20 PF15039 DUF4530: Domain of un 33.6 23 0.00051 22.9 1.0 20 68-87 84-103 (111)
21 TIGR01057 topA_arch DNA topois 33.2 64 0.0014 26.5 3.7 35 8-42 274-309 (618)
22 cd08323 CARD_APAF1 Caspase act 30.6 1.3E+02 0.0028 18.5 4.0 45 28-76 16-71 (86)
23 PF14201 DUF4318: Domain of un 30.1 58 0.0013 19.7 2.3 18 5-22 15-32 (74)
24 PF03202 Lipoprotein_10: Putat 29.8 41 0.0009 22.6 1.8 18 64-81 18-35 (135)
25 COG5587 Uncharacterized conser 29.3 34 0.00074 24.7 1.4 16 64-79 210-225 (228)
26 KOG3824|consensus 29.0 57 0.0012 25.8 2.6 17 60-76 334-350 (472)
27 PF01131 Topoisom_bac: DNA top 28.9 85 0.0018 24.2 3.6 34 9-42 118-153 (403)
28 PRK07220 DNA topoisomerase I; 28.7 78 0.0017 26.7 3.6 33 10-42 279-311 (740)
29 PF02899 Phage_int_SAM_1: Phag 27.6 84 0.0018 17.7 2.7 14 63-76 69-82 (84)
30 PF03172 Sp100: Sp100 domain; 27.0 1.5E+02 0.0031 19.2 3.9 42 30-75 26-67 (103)
31 KOG1991|consensus 26.6 2.5E+02 0.0055 25.0 6.2 73 5-78 518-602 (1010)
32 PF01978 TrmB: Sugar-specific 25.2 1.2E+02 0.0026 16.9 3.1 28 16-43 27-54 (68)
33 PHA00724 hypothetical protein 25.1 34 0.00074 20.9 0.7 13 65-77 69-81 (83)
34 PF11229 DUF3028: Protein of u 24.2 50 0.0011 27.3 1.6 13 64-76 535-547 (589)
35 PRK10022 putative DNA-binding 24.2 1.1E+02 0.0024 21.4 3.2 33 13-46 51-83 (167)
36 PF08331 DUF1730: Domain of un 23.9 82 0.0018 18.6 2.2 19 60-78 49-67 (78)
37 PF05584 Sulfolobus_pRN: Sulfo 22.9 1.4E+02 0.0029 18.1 3.0 22 22-43 29-50 (72)
38 PRK05776 DNA topoisomerase I; 22.7 1.2E+02 0.0027 25.2 3.7 35 8-42 277-312 (670)
39 PRK07219 DNA topoisomerase I; 22.5 1.2E+02 0.0025 25.9 3.6 34 8-41 283-317 (822)
40 PF08064 UME: UME (NUC010) dom 22.4 1.1E+02 0.0023 19.2 2.7 48 4-51 29-80 (107)
41 PF09339 HTH_IclR: IclR helix- 22.3 1.2E+02 0.0025 16.2 2.5 29 15-43 22-50 (52)
42 cd06951 NR_LBD_Dax1_like The l 21.9 2.9E+02 0.0064 19.4 5.2 45 7-52 162-208 (222)
43 PF14357 DUF4404: Domain of un 21.9 1.3E+02 0.0028 18.4 2.9 29 12-40 57-85 (85)
44 cd06936 NR_LBD_Fxr The ligand 21.7 2.6E+02 0.0057 19.6 4.8 43 7-50 162-206 (221)
45 PF05811 DUF842: Eukaryotic pr 21.4 1.2E+02 0.0026 19.9 2.8 35 1-36 92-128 (131)
46 COG5023 Tubulin [Cytoskeleton] 20.7 1.4E+02 0.0031 23.8 3.5 40 41-80 392-431 (443)
47 PF02082 Rrf2: Transcriptional 20.7 1.5E+02 0.0032 17.3 2.9 26 17-42 31-56 (83)
48 PF05068 MtlR: Mannitol repres 20.5 97 0.0021 21.7 2.3 33 13-46 52-84 (170)
49 PF15082 DUF4549: Domain of un 20.3 1.2E+02 0.0027 20.6 2.7 38 3-40 75-112 (144)
50 PF06014 DUF910: Bacterial pro 20.2 1E+02 0.0022 18.1 2.0 21 27-47 29-49 (62)
No 1
>PF02020 W2: eIF4-gamma/eIF5/eIF2-epsilon; InterPro: IPR003307 This entry represents the W2 domain (two invariant tryptophans) and is a region of ~165 amino acids which is found in the C terminus of the following eIFs [, , , ]: Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon) Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included []. The W2 domain has a globular fold and is exclusively composed out of alpha-helices [, , ]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions. For example, the W2 domain of H. sapiens eIF5 binds eIF2-beta, eIF3 and eIF1 [], and therefore plays an important role in multifactor complex assembly. The entry covers the entire W2 domain.; GO: 0005488 binding; PDB: 3D3M_A 3L6A_A 1PAQ_A 2FUL_D 2IU1_A 1UG3_B 3JUI_A.
Probab=99.95 E-value=5e-28 Score=150.39 Aligned_cols=80 Identities=28% Similarity=0.479 Sum_probs=63.2
Q ss_pred ChHHHHHHHHHHHhhcCCChHHHHHHHHHHHhhhccChhHHHHHHhccCC--CCCcHHHHHHHHHHHHHHhcccccCccc
Q psy8137 6 NTPPTATPPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISD--AYPGKGEALFQVNAWLNWLAEAESEEEE 83 (88)
Q Consensus 6 ~~~~~L~alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~il~W~~~~~~--~~~~~~~~~~~~~~fv~WL~eaeeEs~e 83 (88)
.|++||.|||.||.++..+.+.|++||+.||+.|||+|++|++||++.+. ..+++.++|++++|||+||++|+|||++
T Consensus 3 ~Q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~~~~~~~~~~~~~~r~~~~~fi~WL~eaeeE~~e 82 (84)
T PF02020_consen 3 DQVDLLNALEEFCAENPNLMPLFPKILQQLYDEDILEEEAILEWYEDSKPAVDGEGRAKVRKQAQPFIEWLEEAEEESDE 82 (84)
T ss_dssp HHHHHHHHHHHHHHHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC-SSSSCHHHHHHHHHHHHHHHHHHHHCC-----
T ss_pred HHHHHHHHHHHHHHhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhccCccCCC
Confidence 59999999999999987778999999999999999999999999998322 1234566899999999999999999887
Q ss_pred cc
Q psy8137 84 EE 85 (88)
Q Consensus 84 e~ 85 (88)
+|
T Consensus 83 ed 84 (84)
T PF02020_consen 83 ED 84 (84)
T ss_dssp --
T ss_pred CC
Confidence 54
No 2
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=99.90 E-value=4.6e-24 Score=131.95 Aligned_cols=72 Identities=29% Similarity=0.461 Sum_probs=65.5
Q ss_pred CChHHHHHHHHHHHhhcCCChHHHHHHHHHHHhhhccChhHHHHHHhccCCCCCcHHHHHHHHHHHHHHhccc
Q psy8137 5 PNTPPTATPPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALFQVNAWLNWLAEA 77 (88)
Q Consensus 5 ~~~~~~L~alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~il~W~~~~~~~~~~~~~~~~~~~~fv~WL~ea 77 (88)
..|+++|+|||.||.+.+.+.+.++.||+.||+.|||+|++|++||++.+. .+++.+++++++|||+||++|
T Consensus 12 ~~q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~dileEe~il~W~~~~~~-~~~~~~~~~~~~~fv~WL~eA 83 (83)
T smart00515 12 EEQIDLLYAIEEFCVELEKLIKLLPKILKSLYDADILEEEAILKWYEKAVS-AEGKKKVRKNAKPFVTWLQEA 83 (83)
T ss_pred HHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhhhccccHHHHHHHHHcCCC-hHHHHHHHHHHhHHHHHHHcC
Confidence 479999999999999977788999999999999999999999999998763 346788999999999999986
No 3
>KOG2297|consensus
Probab=99.77 E-value=7.2e-19 Score=132.30 Aligned_cols=79 Identities=23% Similarity=0.340 Sum_probs=73.2
Q ss_pred CCCChHHHHHHHHHHHhhcCCChHHHHHHHHHHHhhhccChhHHHHHHhccCCCCCcHHHHHHHHHHHHHHhcccccCcc
Q psy8137 3 PGPNTPPTATPPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALFQVNAWLNWLAEAESEEE 82 (88)
Q Consensus 3 ~~~~~~~~L~alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~il~W~~~~~~~~~~~~~~~~~~~~fv~WL~eaeeEs~ 82 (88)
.|.+-+.+|+.+|.||+++-+.++.|++|+..||..||++|+.|++||.++.... |+.+..++.+|||+||++|||||+
T Consensus 334 ~g~sEL~Ll~KvQe~CYen~~fMKaFqkiV~lfYk~dVLsEe~IL~Wyk~gh~~K-Gk~~FleqmkkFVeWL~~AEEEsE 412 (412)
T KOG2297|consen 334 QGQSELELLLKVQEYCYENIHFMKAFQKIVVLFYKADVLSEETILKWYKEGHVAK-GKSVFLEQMKKFVEWLQNAEEESE 412 (412)
T ss_pred CChHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccc-cHHHHHHHHHHHHHHHHhhhhccC
Confidence 4777889999999999998888999999999999999999999999999987664 889999999999999999999874
No 4
>KOG2767|consensus
Probab=99.72 E-value=1.1e-17 Score=126.57 Aligned_cols=83 Identities=29% Similarity=0.416 Sum_probs=70.0
Q ss_pred CChHHHHHHHHHHHhhcC-CChHHHHHHHHHHHhhhccChhHHHHHHhccCCCCCcH---HHHHHHHHHHHHHhcccccC
Q psy8137 5 PNTPPTATPPELFCHSLH-FPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGK---GEALFQVNAWLNWLAEAESE 80 (88)
Q Consensus 5 ~~~~~~L~alq~~c~~~~-~~~~~~~~il~~LYd~DiveEe~il~W~~~~~~~~~~~---~~~~~~~~~fv~WL~eaeeE 80 (88)
+.|+-+|.+|+.+|..+. -..+.++.||+.||+.||++|+.|+.|+.+++.+++++ .++++.++|||+||++||++
T Consensus 313 k~qr~LLggiE~~~~~~~~el~~kva~ilk~lYd~DI~~e~vi~~w~~K~skk~vsk~~sk~i~e~a~Pfi~WL~~AESe 392 (400)
T KOG2767|consen 313 KAQRYLLGGIERFVEKHEAELISKVAGILKELYDEDILEEEVIIKWGEKPSKKYVSKEKSKKIRENAKPFIEWLKNAESE 392 (400)
T ss_pred HHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHhcccccccchhhhhhhHhhhhHHHHHHHhcccc
Confidence 349999999999998843 23568899999999999999999999999999876554 34799999999999999877
Q ss_pred ccccccc
Q psy8137 81 EEEEEEE 87 (88)
Q Consensus 81 s~ee~ed 87 (88)
++++|+|
T Consensus 393 ~eeEedd 399 (400)
T KOG2767|consen 393 DEEEEDD 399 (400)
T ss_pred ccccccC
Confidence 7776654
No 5
>KOG1461|consensus
Probab=99.68 E-value=7.2e-17 Score=128.91 Aligned_cols=80 Identities=23% Similarity=0.310 Sum_probs=68.5
Q ss_pred ChHHHHHHHHHHHhhcCCChHHHHHHHHHHHhhhccChhHHHHHHhccCCCCCcHHHHHHHHHHHHHHhcccccCccccc
Q psy8137 6 NTPPTATPPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALFQVNAWLNWLAEAESEEEEEE 85 (88)
Q Consensus 6 ~~~~~L~alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~il~W~~~~~~~~~~~~~~~~~~~~fv~WL~eaeeEs~ee~ 85 (88)
.|+++|.+||.+|.+.+...+.+.++++.||+.||++|++|++|+...+...+...+.+.++++||+||++|+|||++||
T Consensus 594 eqid~l~~led~~~e~~~~~~~~~~~v~~lY~~dil~EdaI~~W~~~~~~~~~~~~~~~~~~k~fv~WL~easeE~~~ee 673 (673)
T KOG1461|consen 594 EQIDLLLALEDKCVESEELGPKAAKLVHYLYDYDILQEDAILSWSSQKAGDDEEDAVYNQQLKKFVDWLKEASEEEESEE 673 (673)
T ss_pred HHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHhHhhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHhhcccccccCC
Confidence 59999999999999988778899999999999999999999999988433322234578889999999999999987754
No 6
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=70.90 E-value=5.9 Score=19.87 Aligned_cols=19 Identities=32% Similarity=0.522 Sum_probs=16.4
Q ss_pred HHHHHHHHhhhccChhHHH
Q psy8137 29 LRWFNNLYNLEIIEEEAFS 47 (88)
Q Consensus 29 ~~il~~LYd~DiveEe~il 47 (88)
...|+.||+.++|+++-|.
T Consensus 5 L~~L~~l~~~G~IseeEy~ 23 (31)
T PF09851_consen 5 LEKLKELYDKGEISEEEYE 23 (31)
T ss_pred HHHHHHHHHcCCCCHHHHH
Confidence 3578999999999999885
No 7
>PF00123 Hormone_2: Peptide hormone; InterPro: IPR000532 A number of polypeptidic hormones, mainly expressed in the intestine or the pancreas, belong to a group of structurally related peptides [, ]. Once such hormone, glucagon is widely distributed and produced in the alpha-cells of pancreatic islets []. It affects glucose metabolism in the liver [] by inhibiting glycogen synthesis, stimulating glycogenolysis and enchancing gluconeogenesis. It also increases mobilisation of glucose, free fatty acids and ketone bodies, which are metabolites produced in excess in diabetes mellitus. Glucagon is produced, like other peptide hormones, as part of a larger precursor (preproglucagon), which is cleaved to produce glucagon, glucagon-like protein I and glucagon-like protein II []. The structure of glucagon itself is fully conserved in all known mammalian species []. Other members of the structurally similar group include glicentin precursor, secretin, gastric inhibitory protein, vasoactive intestinal peptide (VIP), prealbumin, peptide HI-27 and growth hormone releasing factor.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1T5Q_A 2OBU_A 2QKH_B 2L70_A 2L71_A 2B4N_A 1GCN_A 1D0R_A 3IOL_B 2RRI_A ....
Probab=68.05 E-value=5.3 Score=19.93 Aligned_cols=12 Identities=25% Similarity=0.736 Sum_probs=9.3
Q ss_pred HHHHHHHHHHhc
Q psy8137 64 LFQVNAWLNWLA 75 (88)
Q Consensus 64 ~~~~~~fv~WL~ 75 (88)
..+++.||+||.
T Consensus 16 ~~aak~fl~~L~ 27 (28)
T PF00123_consen 16 QLAAKKFLQWLM 27 (28)
T ss_dssp HHHHHHHHHHHC
T ss_pred HHHHHHHHHHHh
Confidence 345889999995
No 8
>smart00070 GLUCA Glucagon like hormones.
Probab=60.76 E-value=8.1 Score=19.08 Aligned_cols=12 Identities=25% Similarity=0.736 Sum_probs=9.0
Q ss_pred HHHHHHHHHHhc
Q psy8137 64 LFQVNAWLNWLA 75 (88)
Q Consensus 64 ~~~~~~fv~WL~ 75 (88)
..+++.||.||.
T Consensus 16 ~~~ar~fl~~L~ 27 (27)
T smart00070 16 QLAAKKFLQWLM 27 (27)
T ss_pred HHHHHHHHHHhC
Confidence 344889999983
No 9
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=58.59 E-value=38 Score=20.84 Aligned_cols=48 Identities=10% Similarity=-0.020 Sum_probs=36.2
Q ss_pred CChHHHHHHHHHHHhhcC-CChHHHHHHHHHHHhhhccChhHHHHHHhc
Q psy8137 5 PNTPPTATPPELFCHSLH-FPKGMLLRWFNNLYNLEIIEEEAFSKWREN 52 (88)
Q Consensus 5 ~~~~~~L~alq~~c~~~~-~~~~~~~~il~~LYd~DiveEe~il~W~~~ 52 (88)
..+++++..+=..|.+.. ...+.+..+++.|++.+++....|..=+..
T Consensus 32 ~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~ 80 (113)
T smart00544 32 EQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWR 80 (113)
T ss_pred cchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHH
Confidence 466677777666776653 346789999999999999999988765543
No 10
>PF03271 EB1: EB1-like C-terminal motif; InterPro: IPR004953 A group of microtubule-associated proteins called +TIPs (plus end tracking proteins), including EB1 (end-binding protein 1) family proteins, label growing microtubules ends specifically in diverse organisms and are implicated in spindle dynamics, chromosome segregation, and directing microtubules toward cortical sites. EB1 members have a bipartite composition: the N-terminal CH domain (IPR001715 from INTERPRO) mediates microtubule plus end localization and a C-terminal cargo binding domain (EB1-C) that captures cell polarity determinants. The EB1-C domain comprises a unique EB1-like sequence motif that acts as a binding site for other +TIP proteins. It interacts with the carboxy terminus of the adenomatous polyposis coli (APC) tumor suppressor, a well conserved +TIP phosphoprotein with a pivotal function in cell cycle regulation. Another binding partner of the EB1-C domain is the well conserved +TIP protein dynactin, a component of the large cytoplasmic dynein/dynactin complex [, , ]. The ~80-residue EB1-C domain starts with a long smoothly curved helix (alpha1), which is followed by a hairpin connection leading to a short second helix (alpha2) running antiparallel to alpha1. The two parallel alpha1 helices of the EB1-C domain dimer wrap around each other in a slightly left-handed supercoil. The two alpha2 helices run antiparallel to helices alpha1 and form a similar fork in the opposite orientation and rotated by 90 degrees. As a result, two helical segments from each monomer form a four-helix bundle. The side chain forming the hydrophobic core of this bundle are highly conserved [, , ]. Some protein known to contain an EB1-C domain are listed below: Yeast protein BIM1. Fission yeast microtubule integrity protein mal3. Vertebrate microtubule-associated protein RP/EB family member 1 (EB1). Vertebrate microtubule-associated protein RP/EB family member 2 (EB2 or RP1). Vertebrate microtubule-associated protein RP/EB family member 3 (EBF3). ; GO: 0008017 microtubule binding; PDB: 3TQ7_B 4E61_B 2HKQ_A 1YIG_B 3GJO_B 2HL5_B 1YIB_A 1WU9_A 1TXQ_B.
Probab=52.23 E-value=36 Score=18.35 Aligned_cols=28 Identities=21% Similarity=0.419 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhc----CCChHHHHHHHHHHHh
Q psy8137 10 TATPPELFCHSL----HFPKGMLLRWFNNLYN 37 (88)
Q Consensus 10 ~L~alq~~c~~~----~~~~~~~~~il~~LYd 37 (88)
-|..|+.+|... ..+..+...|+..||.
T Consensus 12 KLR~IE~l~q~~~~~~~~~~~~~~~I~~ILYa 43 (43)
T PF03271_consen 12 KLRDIEILCQEANESENEPKDLIKKIQEILYA 43 (43)
T ss_dssp HHHHHHHHHHHHCHHCCTC--HHHHHHHHHHC
T ss_pred HHHHHHHHHhhccccCcchhHHHHHHHHHhcC
Confidence 478889999882 1223367888888883
No 11
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=47.71 E-value=29 Score=25.32 Aligned_cols=33 Identities=15% Similarity=0.170 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhc-CCChHHHHHHHHHHHhhhccC
Q psy8137 10 TATPPELFCHSL-HFPKGMLLRWFNNLYNLEIIE 42 (88)
Q Consensus 10 ~L~alq~~c~~~-~~~~~~~~~il~~LYd~Dive 42 (88)
-|..||..|... .........|.+.||+..+|+
T Consensus 14 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYe~g~iT 47 (259)
T smart00437 14 TTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLIT 47 (259)
T ss_pred cHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCeeE
Confidence 467889999884 444557788999999976654
No 12
>PF09090 MIF4G_like_2: MIF4G like; InterPro: IPR015174 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 2", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=45.54 E-value=43 Score=24.17 Aligned_cols=45 Identities=18% Similarity=0.073 Sum_probs=33.3
Q ss_pred ChHHHHHHHHHHHhhcCCChHHHHHHHHHHHhhhccChhHHHHHHhcc
Q psy8137 6 NTPPTATPPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAFSKWRENI 53 (88)
Q Consensus 6 ~~~~~L~alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~il~W~~~~ 53 (88)
.|..+|.++-.|=.++. .....|+..|-..+||+-.+|..|-=+.
T Consensus 92 ~q~~il~~v~~~W~~~~---q~~~li~dkll~~~ii~~~~Vv~w~f~~ 136 (253)
T PF09090_consen 92 AQFWILDAVFRFWKNNP---QMGFLIIDKLLNYGIISPSAVVNWVFSP 136 (253)
T ss_dssp HHHHHHHHHHHHHTT-H---HHHHHHHHHHHHTTSS-HHHHHHHHTSG
T ss_pred HHHHHHHHHHHHHhcCC---ceehHHHHHHHhcCCCCHHHHHHHHcCc
Confidence 46777777777765533 3666788899999999999999999543
No 13
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=44.31 E-value=71 Score=19.26 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhhhccChhHHHHHHhccCCCCCcHHHHHH-----------HHHHHHHHhccc
Q psy8137 27 MLLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALF-----------QVNAWLNWLAEA 77 (88)
Q Consensus 27 ~~~~il~~LYd~DiveEe~il~W~~~~~~~~~~~~~~~~-----------~~~~fv~WL~ea 77 (88)
.+..|+-.||..+||.++..-.=...+.. ..++|+ +...|++.|++-
T Consensus 16 ~v~~ilD~L~~~~Vit~e~~~~I~a~~T~----~~kar~Lld~l~~kG~~A~~~F~~~L~e~ 73 (82)
T cd08330 16 NVDPILDKLHGKKVITQEQYSEVRAEKTN----QEKMRKLFSFVRSWGASCKDIFYQILREE 73 (82)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHcCCCc----HHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence 35678999999999999987655544322 122222 234688888754
No 14
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=41.68 E-value=38 Score=25.98 Aligned_cols=33 Identities=18% Similarity=0.203 Sum_probs=24.7
Q ss_pred HHHHHHHHHhhc-CCChHHHHHHHHHHHhhhccC
Q psy8137 10 TATPPELFCHSL-HFPKGMLLRWFNNLYNLEIIE 42 (88)
Q Consensus 10 ~L~alq~~c~~~-~~~~~~~~~il~~LYd~Dive 42 (88)
-|..||..|... .........+.+.||+.++|+
T Consensus 88 ~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYe~glIS 121 (381)
T cd00186 88 TTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLIT 121 (381)
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCeee
Confidence 467889999874 444557779999999986554
No 15
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=37.58 E-value=56 Score=19.95 Aligned_cols=45 Identities=9% Similarity=0.008 Sum_probs=30.3
Q ss_pred ChHHHHHHHHHHHhhc-CCChHHHHHHHHHHHhhhccChhHHHHHH
Q psy8137 6 NTPPTATPPELFCHSL-HFPKGMLLRWFNNLYNLEIIEEEAFSKWR 50 (88)
Q Consensus 6 ~~~~~L~alq~~c~~~-~~~~~~~~~il~~LYd~DiveEe~il~W~ 50 (88)
..+.++..+=..|.+. ......+..++..|+..+++..+.|..=+
T Consensus 33 ~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf 78 (113)
T PF02847_consen 33 QHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGF 78 (113)
T ss_dssp GHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHH
T ss_pred cHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence 3445555555555554 33346888999999999999999987544
No 16
>PF03801 Ndc80_HEC: HEC/Ndc80p family; InterPro: IPR005550 Members of this family are components of the mitotic spindle. It has been shown that Ndc80 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle.; PDB: 3IZ0_E 2VE7_B 2IGP_A.
Probab=37.07 E-value=90 Score=21.11 Aligned_cols=32 Identities=16% Similarity=0.148 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHhhcCC-C------------hHHHHHHHHHHHhh
Q psy8137 7 TPPTATPPELFCHSLHF-P------------KGMLLRWFNNLYNL 38 (88)
Q Consensus 7 ~~~~L~alq~~c~~~~~-~------------~~~~~~il~~LYd~ 38 (88)
|..|+..|..|...+.+ + .+.|..|++.||..
T Consensus 38 q~~~~~~I~~fL~~~~~~~~~is~k~l~~Pt~kdf~~I~~fL~~~ 82 (157)
T PF03801_consen 38 QQECIRKIYEFLSEHGFESHPISPKTLKSPTQKDFVEIFNFLFRQ 82 (157)
T ss_dssp HHHHHHHHHHHHHHTT--SS---TTTTSS--HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcCCCCccccccccCCCCHHHHHHHHHHHHHH
Confidence 88999999999977554 1 14788999999987
No 17
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=35.06 E-value=1.1e+02 Score=18.93 Aligned_cols=48 Identities=13% Similarity=0.243 Sum_probs=30.0
Q ss_pred HHHHHHHHHhhhccChhHHHHHHhccCCCCCcHHH-----H----HHHHHHHHHHhccc
Q psy8137 28 LLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGE-----A----LFQVNAWLNWLAEA 77 (88)
Q Consensus 28 ~~~il~~LYd~DiveEe~il~W~~~~~~~~~~~~~-----~----~~~~~~fv~WL~ea 77 (88)
...|+..||..+|+.++..-.=...+... .+.. + ..+...|++.|++-
T Consensus 25 v~~ilD~Ll~~~Vlt~ee~e~I~~~~t~~--~qAr~Lld~l~~KG~~A~~~F~~~L~e~ 81 (94)
T cd08329 25 VLPILDSLLSANVITEQEYDVIKQKTQTP--LQARELIDTVLVKGNAAAEVFRNCLKKN 81 (94)
T ss_pred hHHHHHHHHHcCCCCHHHHHHHHcCCChH--HHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence 34588999999999999886555443321 1111 1 22255699999754
No 18
>KOG3021|consensus
Probab=34.07 E-value=53 Score=24.78 Aligned_cols=19 Identities=11% Similarity=0.018 Sum_probs=17.0
Q ss_pred CCCCChHHHHHHHHHHHhh
Q psy8137 2 DPGPNTPPTATPPELFCHS 20 (88)
Q Consensus 2 ~~~~~~~~~L~alq~~c~~ 20 (88)
-||.+|+-.||-|=.|..+
T Consensus 270 a~G~eqR~~LYqLyhyLNH 288 (313)
T KOG3021|consen 270 APGFEQRLLLYQLYHYLNH 288 (313)
T ss_pred CCcHHHHHHHHHHHHHhhh
Confidence 4899999999999999888
No 19
>PRK11001 mtlR mannitol repressor protein; Provisional
Probab=33.77 E-value=74 Score=22.34 Aligned_cols=34 Identities=26% Similarity=0.323 Sum_probs=25.1
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhhhccChhHH
Q psy8137 12 TPPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAF 46 (88)
Q Consensus 12 ~alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~i 46 (88)
+|++-+..+.+ |-+.+..-++.+|-.++|+.+.+
T Consensus 49 yaVePLL~~~G-PLg~lsVRLKLlygLGvIs~~~Y 82 (171)
T PRK11001 49 YAVEPLLDGDG-PLGDLSVRLKLLYGLGVISREEY 82 (171)
T ss_pred HHHHHHhcCCC-CchhHHHHHHHHHHccCCCHHHH
Confidence 34444444444 67788999999999999998764
No 20
>PF15039 DUF4530: Domain of unknown function (DUF4530)
Probab=33.59 E-value=23 Score=22.87 Aligned_cols=20 Identities=45% Similarity=0.611 Sum_probs=13.7
Q ss_pred HHHHHHhcccccCccccccc
Q psy8137 68 NAWLNWLAEAESEEEEEEEE 87 (88)
Q Consensus 68 ~~fv~WL~eaeeEs~ee~ed 87 (88)
...++-|++.+++|++++++
T Consensus 84 eElvt~lEEEee~s~e~ee~ 103 (111)
T PF15039_consen 84 EELVTILEEEEEESEEEEED 103 (111)
T ss_pred HHHHHHhHHhhccccchhhh
Confidence 35678888877777665554
No 21
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=33.19 E-value=64 Score=26.46 Aligned_cols=35 Identities=14% Similarity=0.097 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhhc-CCChHHHHHHHHHHHhhhccC
Q psy8137 8 PPTATPPELFCHSL-HFPKGMLLRWFNNLYNLEIIE 42 (88)
Q Consensus 8 ~~~L~alq~~c~~~-~~~~~~~~~il~~LYd~Dive 42 (88)
+=-|..||..|... .........+.+.||+..+|+
T Consensus 274 pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYe~g~IS 309 (618)
T TIGR01057 274 PFDLGTLQREAYRIFGFSPKKTQSIAQELYEEALIS 309 (618)
T ss_pred CccHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCcee
Confidence 33478899999874 444456779999999976554
No 22
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=30.57 E-value=1.3e+02 Score=18.49 Aligned_cols=45 Identities=9% Similarity=0.097 Sum_probs=29.7
Q ss_pred HHHHHHHHHhhhccChhHHHHHHhccCCCCCcHHHHH-----------HHHHHHHHHhcc
Q psy8137 28 LLRWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEAL-----------FQVNAWLNWLAE 76 (88)
Q Consensus 28 ~~~il~~LYd~DiveEe~il~W~~~~~~~~~~~~~~~-----------~~~~~fv~WL~e 76 (88)
...|+..||..+|++++.+-.=...+... .+++ .+...|.++|++
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~~t~~----~qa~~Lld~L~trG~~Af~~F~~aL~~ 71 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSKATQK----EKAVMLINMILTKDNHAYVSFYNALLH 71 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcCCChH----HHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence 45689999999999999886555443321 1221 124468999985
No 23
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=30.08 E-value=58 Score=19.71 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=15.5
Q ss_pred CChHHHHHHHHHHHhhcC
Q psy8137 5 PNTPPTATPPELFCHSLH 22 (88)
Q Consensus 5 ~~~~~~L~alq~~c~~~~ 22 (88)
||-..+..||+.||.++.
T Consensus 15 Ps~e~i~~aIE~YC~~~~ 32 (74)
T PF14201_consen 15 PSKEEICEAIEKYCIKNG 32 (74)
T ss_pred CCHHHHHHHHHHHHHHcC
Confidence 577889999999999955
No 24
>PF03202 Lipoprotein_10: Putative mycoplasma lipoprotein, C-terminal region; InterPro: IPR004890 This domain is found along with a central domain (IPR004984 from INTERPRO) in a group of Mycoplasma lipoproteins of unknown function.
Probab=29.77 E-value=41 Score=22.59 Aligned_cols=18 Identities=17% Similarity=0.337 Sum_probs=13.7
Q ss_pred HHHHHHHHHHhcccccCc
Q psy8137 64 LFQVNAWLNWLAEAESEE 81 (88)
Q Consensus 64 ~~~~~~fv~WL~eaeeEs 81 (88)
-+.++.||.||-...++.
T Consensus 18 D~aTkkFv~Wll~~~~~~ 35 (135)
T PF03202_consen 18 DKATKKFVNWLLNSKETW 35 (135)
T ss_pred cHHHHHHHHHHHcCcccc
Confidence 456889999998776543
No 25
>COG5587 Uncharacterized conserved protein [Function unknown]
Probab=29.25 E-value=34 Score=24.67 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=13.0
Q ss_pred HHHHHHHHHHhccccc
Q psy8137 64 LFQVNAWLNWLAEAES 79 (88)
Q Consensus 64 ~~~~~~fv~WL~eaee 79 (88)
...+.|||+|++-+++
T Consensus 210 ~~ra~PliDw~ra~e~ 225 (228)
T COG5587 210 LHRAAPLIDWLRAAED 225 (228)
T ss_pred HHHhhhHHHHHHHHhc
Confidence 4558899999998764
No 26
>KOG3824|consensus
Probab=29.00 E-value=57 Score=25.78 Aligned_cols=17 Identities=18% Similarity=0.603 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHhcc
Q psy8137 60 KGEALFQVNAWLNWLAE 76 (88)
Q Consensus 60 ~~~~~~~~~~fv~WL~e 76 (88)
...+.++.+.|++||..
T Consensus 334 P~dv~~qmq~fv~WLNs 350 (472)
T KOG3824|consen 334 PEDVMEQMQDFVDWLNS 350 (472)
T ss_pred hHHHHHHHHHHHHHhcc
Confidence 35689999999999984
No 27
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=28.93 E-value=85 Score=24.16 Aligned_cols=34 Identities=15% Similarity=0.080 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhc-CCChHHHHHHHHHHHhh-hccC
Q psy8137 9 PTATPPELFCHSL-HFPKGMLLRWFNNLYNL-EIIE 42 (88)
Q Consensus 9 ~~L~alq~~c~~~-~~~~~~~~~il~~LYd~-Dive 42 (88)
=-|..||..|... .........+++.||+. .+|+
T Consensus 118 ~~l~~Lq~~a~k~~g~s~~~tl~iaQ~LYE~~g~IS 153 (403)
T PF01131_consen 118 FNLSTLQKEASKKLGFSAKETLDIAQKLYEKHGLIS 153 (403)
T ss_dssp B-HHHHHHHHHHHH---HHHHHHHHHHHHHTTTSBS
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhheee
Confidence 3567888888884 44455778899999996 8776
No 28
>PRK07220 DNA topoisomerase I; Validated
Probab=28.72 E-value=78 Score=26.66 Aligned_cols=33 Identities=21% Similarity=0.192 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhcCCChHHHHHHHHHHHhhhccC
Q psy8137 10 TATPPELFCHSLHFPKGMLLRWFNNLYNLEIIE 42 (88)
Q Consensus 10 ~L~alq~~c~~~~~~~~~~~~il~~LYd~Dive 42 (88)
-+..||..|....+.......|.+.||+.++|+
T Consensus 279 ~ts~Lq~~a~~~g~s~~~tm~iaQ~LYe~g~IT 311 (740)
T PRK07220 279 NTTEFISAANSIGFSAANAMRIAESLYTNGYIS 311 (740)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHhCCcee
Confidence 467788888876655567789999999975553
No 29
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=27.57 E-value=84 Score=17.72 Aligned_cols=14 Identities=21% Similarity=0.396 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHhcc
Q psy8137 63 ALFQVNAWLNWLAE 76 (88)
Q Consensus 63 ~~~~~~~fv~WL~e 76 (88)
.+..++.|..||..
T Consensus 69 ~~~alr~f~~~l~~ 82 (84)
T PF02899_consen 69 RLSALRAFFRFLYR 82 (84)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 56678899999864
No 30
>PF03172 Sp100: Sp100 domain; InterPro: IPR004865 The Sp100 and promyelocytic leukemia proteins (PML) are constituents of nuclear domains, known as nuclear dots (NDs or NBs - nuclear bodies or PML bodies), and are both covalently modified by the small ubiquitin-related protein SUMO-1. NBs play a role in autoimmunity, virus infections, and in the etiology of acute promyelocytic leukemia []. A functional nuclear localization signal and an NB-targeting region that coincides with an Sp100 homodimerization domain have been mapped. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins, which include the autoimmune regulator proteins (AIRE) and other numerous other transiently or permanently localised proteins. PML is expressed as a family of isoforms (PML I-VII) as a result of alternative splicing, most of which are found in the nucleus. Although there are many other functions of PML NBs in a wide range of cellular pathways, there is accumulating evidence that they represent preferential targets for viral infections and that PML plays a role in the mechanism of the antiviral action of interferon []. The Sp100 domain is usually found at the amino terminus of proteins that contain a SAND domain IPR000770 from INTERPRO. ; GO: 0005634 nucleus
Probab=26.98 E-value=1.5e+02 Score=19.22 Aligned_cols=42 Identities=19% Similarity=0.312 Sum_probs=27.7
Q ss_pred HHHHHHHhhhccChhHHHHHHhccCCCCCcHHHHHHHHHHHHHHhc
Q psy8137 30 RWFNNLYNLEIIEEEAFSKWRENISDAYPGKGEALFQVNAWLNWLA 75 (88)
Q Consensus 30 ~il~~LYd~DiveEe~il~W~~~~~~~~~~~~~~~~~~~~fv~WL~ 75 (88)
..|+.|-|.++|.|..+..=.+.-.... + +.+.+=..++||+
T Consensus 26 Pfl~gLrD~~~ItE~~y~e~~e~crnlv-p---v~rvvY~vLs~Le 67 (103)
T PF03172_consen 26 PFLEGLRDHSFITEQMYKESQEACRNLV-P---VQRVVYNVLSWLE 67 (103)
T ss_pred hHHHHhhhcccccHHHHHHHHHHHhccc-c---HHHHHHHHHHHHH
Confidence 4678899999999999876554422221 1 4444555677774
No 31
>KOG1991|consensus
Probab=26.61 E-value=2.5e+02 Score=25.00 Aligned_cols=73 Identities=11% Similarity=0.064 Sum_probs=40.9
Q ss_pred CChHHHHHHHHHHHhhcCCC----hH----HHHHHHH--HHHhhhccCh--hHHHHHHhccCCCCCcHHHHHHHHHHHHH
Q psy8137 5 PNTPPTATPPELFCHSLHFP----KG----MLLRWFN--NLYNLEIIEE--EAFSKWRENISDAYPGKGEALFQVNAWLN 72 (88)
Q Consensus 5 ~~~~~~L~alq~~c~~~~~~----~~----~~~~il~--~LYd~DiveE--e~il~W~~~~~~~~~~~~~~~~~~~~fv~ 72 (88)
|-++++-.|||.|....... .+ ++..+|+ .=|+.|.++. +.|..=|...-++. +..-+...++.|..
T Consensus 518 PV~VeAalALq~fI~~~~~~~e~~~~hvp~~mq~lL~L~ne~End~Lt~vme~iV~~fseElsPf-A~eL~q~La~~F~k 596 (1010)
T KOG1991|consen 518 PVRVEAALALQSFISNQEQADEKVSAHVPPIMQELLKLSNEVENDDLTNVMEKIVCKFSEELSPF-AVELCQNLAETFLK 596 (1010)
T ss_pred chhhHHHHHHHHHHhcchhhhhhHhhhhhHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHhhchh-HHHHHHHHHHHHHH
Confidence 67888999999999884421 22 3333333 2345555543 34444443322222 12335566778999
Q ss_pred Hhcccc
Q psy8137 73 WLAEAE 78 (88)
Q Consensus 73 WL~eae 78 (88)
-|++.+
T Consensus 597 ~l~~~~ 602 (1010)
T KOG1991|consen 597 VLQTSE 602 (1010)
T ss_pred HHhccC
Confidence 999733
No 32
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=25.21 E-value=1.2e+02 Score=16.89 Aligned_cols=28 Identities=14% Similarity=0.259 Sum_probs=21.3
Q ss_pred HHHhhcCCChHHHHHHHHHHHhhhccCh
Q psy8137 16 LFCHSLHFPKGMLLRWFNNLYNLEIIEE 43 (88)
Q Consensus 16 ~~c~~~~~~~~~~~~il~~LYd~DiveE 43 (88)
..+...+.+.+.+..+|+.|.+.++|.-
T Consensus 27 eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 27 EIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 3444556677788899999999999864
No 33
>PHA00724 hypothetical protein
Probab=25.08 E-value=34 Score=20.92 Aligned_cols=13 Identities=31% Similarity=0.764 Sum_probs=9.4
Q ss_pred HHHHHHHHHhccc
Q psy8137 65 FQVNAWLNWLAEA 77 (88)
Q Consensus 65 ~~~~~fv~WL~ea 77 (88)
....=|++||+|.
T Consensus 69 ~n~~fffnwlree 81 (83)
T PHA00724 69 INFAFFFNWLREE 81 (83)
T ss_pred HHHHHHHHHHHHh
Confidence 3455699999964
No 34
>PF11229 DUF3028: Protein of unknown function (DUF3028); InterPro: IPR021392 This eukaryotic family of proteins has no known function.
Probab=24.24 E-value=50 Score=27.35 Aligned_cols=13 Identities=23% Similarity=0.557 Sum_probs=10.7
Q ss_pred HHHHHHHHHHhcc
Q psy8137 64 LFQVNAWLNWLAE 76 (88)
Q Consensus 64 ~~~~~~fv~WL~e 76 (88)
++++++||+||-.
T Consensus 535 k~qt~kfidwl~s 547 (589)
T PF11229_consen 535 KEQTQKFIDWLFS 547 (589)
T ss_pred HHHHHHHHHHHHH
Confidence 6678999999964
No 35
>PRK10022 putative DNA-binding transcriptional regulator; Provisional
Probab=24.20 E-value=1.1e+02 Score=21.42 Aligned_cols=33 Identities=9% Similarity=0.066 Sum_probs=23.7
Q ss_pred HHHHHHhhcCCChHHHHHHHHHHHhhhccChhHH
Q psy8137 13 PPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAF 46 (88)
Q Consensus 13 alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~i 46 (88)
|++-...+.+ |-+.+..-++.+|-.++|+-+.+
T Consensus 51 aVePLL~~~G-PL~dlsVRLKLl~gLGvIs~~~Y 83 (167)
T PRK10022 51 AVKPLLAQSG-PLDDIDVALRLIYALGKMDKWLY 83 (167)
T ss_pred hhhHhhcCCC-CcchhhhHHHHHHHccCCcHHHH
Confidence 3333443334 66788889999999999998764
No 36
>PF08331 DUF1730: Domain of unknown function (DUF1730); InterPro: IPR013542 This domain of unknown function occurs in iron-sulphur cluster-binding proteins together with the 4Fe-4S binding domain (IPR001450 from INTERPRO).
Probab=23.91 E-value=82 Score=18.60 Aligned_cols=19 Identities=11% Similarity=0.212 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHhcccc
Q psy8137 60 KGEALFQVNAWLNWLAEAE 78 (88)
Q Consensus 60 ~~~~~~~~~~fv~WL~eae 78 (88)
+.+++++++.+.+||++.-
T Consensus 49 H~vlk~~L~~l~~~i~~~~ 67 (78)
T PF08331_consen 49 HKVLKKKLEQLAEWIRELG 67 (78)
T ss_pred HHHHHHHHHHHHHHHHHHC
Confidence 4668999999999999764
No 37
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=22.95 E-value=1.4e+02 Score=18.09 Aligned_cols=22 Identities=32% Similarity=0.424 Sum_probs=18.2
Q ss_pred CCChHHHHHHHHHHHhhhccCh
Q psy8137 22 HFPKGMLLRWFNNLYNLEIIEE 43 (88)
Q Consensus 22 ~~~~~~~~~il~~LYd~DiveE 43 (88)
...++.+...|..|++.+||+.
T Consensus 29 gi~k~~LlV~LsrL~k~GiI~R 50 (72)
T PF05584_consen 29 GISKNTLLVYLSRLAKRGIIER 50 (72)
T ss_pred CCCHHHHHHHHHHHHHCCCeee
Confidence 4456788999999999999975
No 38
>PRK05776 DNA topoisomerase I; Provisional
Probab=22.69 E-value=1.2e+02 Score=25.24 Aligned_cols=35 Identities=14% Similarity=0.076 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhhc-CCChHHHHHHHHHHHhhhccC
Q psy8137 8 PPTATPPELFCHSL-HFPKGMLLRWFNNLYNLEIIE 42 (88)
Q Consensus 8 ~~~L~alq~~c~~~-~~~~~~~~~il~~LYd~Dive 42 (88)
+=-+..||..|... .+.......|.+.||+.++|+
T Consensus 277 pf~ts~LQ~~As~~lg~sa~ktm~iAQ~LYe~glIS 312 (670)
T PRK05776 277 PFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLIS 312 (670)
T ss_pred CCCHHHHHHHHHhhcCCCHHHHHHHHHHHHhcCcee
Confidence 33577889999874 444557788999999975543
No 39
>PRK07219 DNA topoisomerase I; Validated
Probab=22.54 E-value=1.2e+02 Score=25.94 Aligned_cols=34 Identities=15% Similarity=0.073 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhhc-CCChHHHHHHHHHHHhhhcc
Q psy8137 8 PPTATPPELFCHSL-HFPKGMLLRWFNNLYNLEII 41 (88)
Q Consensus 8 ~~~L~alq~~c~~~-~~~~~~~~~il~~LYd~Div 41 (88)
+=-|..||..|... .+.......|.+.||+.++|
T Consensus 283 pf~t~~Lq~~a~~~~g~sa~~tm~iaQ~LYe~glI 317 (822)
T PRK07219 283 PFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYI 317 (822)
T ss_pred CccHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCce
Confidence 33477889999885 44455777899999996443
No 40
>PF08064 UME: UME (NUC010) domain; InterPro: IPR012993 This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1 [].; GO: 0004674 protein serine/threonine kinase activity
Probab=22.45 E-value=1.1e+02 Score=19.25 Aligned_cols=48 Identities=15% Similarity=0.114 Sum_probs=31.0
Q ss_pred CCChHHHHHHHHHHHhhc-CCChHHHHHH---HHHHHhhhccChhHHHHHHh
Q psy8137 4 GPNTPPTATPPELFCHSL-HFPKGMLLRW---FNNLYNLEIIEEEAFSKWRE 51 (88)
Q Consensus 4 ~~~~~~~L~alq~~c~~~-~~~~~~~~~i---l~~LYd~DiveEe~il~W~~ 51 (88)
-..++.+|.+|+.++.-. .+.....++| |+.--+.+=+.+.++-.|..
T Consensus 29 ~~ek~~~l~si~~lI~~~~~~i~~~~pQI~a~L~sal~~~~l~~~al~~W~~ 80 (107)
T PF08064_consen 29 IPEKKRALRSIEELIKLGGSHISSARPQIMACLQSALEIPELREEALSCWNC 80 (107)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHH
Confidence 345788999999998842 2223344444 44444566677888888884
No 41
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=22.33 E-value=1.2e+02 Score=16.19 Aligned_cols=29 Identities=21% Similarity=0.340 Sum_probs=20.4
Q ss_pred HHHHhhcCCChHHHHHHHHHHHhhhccCh
Q psy8137 15 ELFCHSLHFPKGMLLRWFNNLYNLEIIEE 43 (88)
Q Consensus 15 q~~c~~~~~~~~~~~~il~~LYd~DiveE 43 (88)
...+...+.+++....+++.|-+.++|..
T Consensus 22 ~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 22 SEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 44455556667788889999998888764
No 42
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=21.92 E-value=2.9e+02 Score=19.42 Aligned_cols=45 Identities=13% Similarity=-0.059 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHhhcCCCh--HHHHHHHHHHHhhhccChhHHHHHHhc
Q psy8137 7 TPPTATPPELFCHSLHFPK--GMLLRWFNNLYNLEIIEEEAFSKWREN 52 (88)
Q Consensus 7 ~~~~L~alq~~c~~~~~~~--~~~~~il~~LYd~DiveEe~il~W~~~ 52 (88)
|-.++.||+.||.... |. ..|.++|..|=..--+...++.+++-.
T Consensus 162 Qe~~~~aL~~yi~~~~-p~~~~Rf~kLLl~Lp~LRsl~~~~~e~lff~ 208 (222)
T cd06951 162 QKEAQQALNEHTMMTR-PLEQLRSARLLLMLSLLRGIKTEPVTELFFR 208 (222)
T ss_pred HHHHHHHHHHHHHhhC-CCcccHHHHHHHHhHHhhcCCHHHHHHHhCc
Confidence 5567799999997643 32 378899998888888888888887744
No 43
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=21.86 E-value=1.3e+02 Score=18.35 Aligned_cols=29 Identities=28% Similarity=0.253 Sum_probs=20.6
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhhhc
Q psy8137 12 TPPELFCHSLHFPKGMLLRWFNNLYNLEI 40 (88)
Q Consensus 12 ~alq~~c~~~~~~~~~~~~il~~LYd~Di 40 (88)
.|++.|-.++....+.+..|+..|-+.+|
T Consensus 57 ~av~~FE~~HP~l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 57 EAVERFEASHPKLAGILRNIMDSLANMGI 85 (85)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHHHHCCC
Confidence 46666777766656788888888877664
No 44
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=21.72 E-value=2.6e+02 Score=19.60 Aligned_cols=43 Identities=16% Similarity=0.267 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHHhhcCCCh--HHHHHHHHHHHhhhccChhHHHHHH
Q psy8137 7 TPPTATPPELFCHSLHFPK--GMLLRWFNNLYNLEIIEEEAFSKWR 50 (88)
Q Consensus 7 ~~~~L~alq~~c~~~~~~~--~~~~~il~~LYd~DiveEe~il~W~ 50 (88)
|-.++.||+.||.... |. ..|..+|..|=..--+....+-.+.
T Consensus 162 Q~~~~~aL~~y~~~~~-p~~p~rf~~LL~~L~~LR~l~~~~~e~l~ 206 (221)
T cd06936 162 QEPLLDLLQKFCKLYH-PEDPQHFACLLGRLTELRTLNHHHAEMLM 206 (221)
T ss_pred HHHHHHHHHHHHHhhC-CCchhHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 5667789999997643 32 3777888777766666665555443
No 45
>PF05811 DUF842: Eukaryotic protein of unknown function (DUF842); InterPro: IPR008560 This family consists of a number of conserved eukaryotic proteins of unknown function. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation.
Probab=21.42 E-value=1.2e+02 Score=19.92 Aligned_cols=35 Identities=20% Similarity=0.226 Sum_probs=24.5
Q ss_pred CCCCCChHHHHHHHHHHHhh--cCCChHHHHHHHHHHH
Q psy8137 1 MDPGPNTPPTATPPELFCHS--LHFPKGMLLRWFNNLY 36 (88)
Q Consensus 1 ~~~~~~~~~~L~alq~~c~~--~~~~~~~~~~il~~LY 36 (88)
|+|++++.++-..++..+.. .. ..+++|.|.+.|-
T Consensus 92 ~~~~~~~~~~~~~~e~C~~~Cvd~-hi~llP~l~~r~k 128 (131)
T PF05811_consen 92 MDPNPNESDAEKQLESCVNKCVDD-HIKLLPSLTKRMK 128 (131)
T ss_pred ccCCCCchHHHHHHHHHHHHHHHH-HHHHhHHHHHHHH
Confidence 46888888887777777666 23 2457888887663
No 46
>COG5023 Tubulin [Cytoskeleton]
Probab=20.69 E-value=1.4e+02 Score=23.83 Aligned_cols=40 Identities=20% Similarity=0.126 Sum_probs=25.4
Q ss_pred cChhHHHHHHhccCCCCCcHHHHHHHHHHHHHHhcccccC
Q psy8137 41 IEEEAFSKWRENISDAYPGKGEALFQVNAWLNWLAEAESE 80 (88)
Q Consensus 41 veEe~il~W~~~~~~~~~~~~~~~~~~~~fv~WL~eaeeE 80 (88)
..--||+.||..-.-.....+.+|.-++..++=-++++..
T Consensus 392 f~krAFlhwY~~egmee~EFsEare~~~~L~~eY~~~~~~ 431 (443)
T COG5023 392 FKKRAFLHWYVGEGMEEGEFSEAREDVADLEEEYEAAEQD 431 (443)
T ss_pred HHhhHHHHHHhhccCcccchhhHHHHHHHHHHHHHHhccc
Confidence 3457999999774433334455677777666666666544
No 47
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=20.67 E-value=1.5e+02 Score=17.35 Aligned_cols=26 Identities=19% Similarity=0.291 Sum_probs=18.3
Q ss_pred HHhhcCCChHHHHHHHHHHHhhhccC
Q psy8137 17 FCHSLHFPKGMLLRWFNNLYNLEIIE 42 (88)
Q Consensus 17 ~c~~~~~~~~~~~~il~~LYd~Dive 42 (88)
.+.....+...+.+|++.|-..++|.
T Consensus 31 iA~~~~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 31 IAERLGISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence 33333445568899999999999985
No 48
>PF05068 MtlR: Mannitol repressor; InterPro: IPR007761 The mannitol operon of Escherichia coli, encoding the mannitol-specific enzyme II of the phosphotransferase system (MtlA) and mannitol phosphate dehydrogenase (MtlD) contains an additional downstream open reading frame which encodes the mannitol repressor (MtlR).; PDB: 3C8G_C 3BRJ_D.
Probab=20.45 E-value=97 Score=21.70 Aligned_cols=33 Identities=24% Similarity=0.346 Sum_probs=22.6
Q ss_pred HHHHHHhhcCCChHHHHHHHHHHHhhhccChhHH
Q psy8137 13 PPELFCHSLHFPKGMLLRWFNNLYNLEIIEEEAF 46 (88)
Q Consensus 13 alq~~c~~~~~~~~~~~~il~~LYd~DiveEe~i 46 (88)
+++-+..+.+ |-+.|..-++.+|-.++|+...+
T Consensus 52 vVepLl~~~G-PL~~~svRlKL~y~LG~Is~~~y 84 (170)
T PF05068_consen 52 VVEPLLSGSG-PLGTFSVRLKLLYALGLISKEEY 84 (170)
T ss_dssp CHHHHHSTTS-TTSSHHHHHHHHHHTT-S-HHHH
T ss_pred HHHHHhcCCC-CchhHHHHHHHHHHcCCCCHHHH
Confidence 3444444444 67788999999999999998754
No 49
>PF15082 DUF4549: Domain of unknown function (DUF4549)
Probab=20.33 E-value=1.2e+02 Score=20.65 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=24.3
Q ss_pred CCCChHHHHHHHHHHHhhcCCChHHHHHHHHHHHhhhc
Q psy8137 3 PGPNTPPTATPPELFCHSLHFPKGMLLRWFNNLYNLEI 40 (88)
Q Consensus 3 ~~~~~~~~L~alq~~c~~~~~~~~~~~~il~~LYd~Di 40 (88)
|-.+|-+++.-=-.-|...+.....+|.+|+.+|-.-|
T Consensus 75 PLviQadvmqrElEscl~~Eyt~~~LPLLLhQfy~~ri 112 (144)
T PF15082_consen 75 PLVIQADVMQRELESCLRREYTPENLPLLLHQFYTDRI 112 (144)
T ss_pred chhHHHHHHHHHHHHHhhhccCccccHHHHHHHHHHHH
Confidence 44566666655455566666555677888888776544
No 50
>PF06014 DUF910: Bacterial protein of unknown function (DUF910); InterPro: IPR009256 This family consists of several short bacterial proteins of unknown function.; PDB: 2NN4_A.
Probab=20.19 E-value=1e+02 Score=18.15 Aligned_cols=21 Identities=14% Similarity=0.389 Sum_probs=15.5
Q ss_pred HHHHHHHHHHhhhccChhHHH
Q psy8137 27 MLLRWFNNLYNLEIIEEEAFS 47 (88)
Q Consensus 27 ~~~~il~~LYd~DiveEe~il 47 (88)
++..=++.||+.++|+.+.++
T Consensus 29 lM~~El~~Ly~~~lidk~~y~ 49 (62)
T PF06014_consen 29 LMEIELKELYKSGLIDKKEYL 49 (62)
T ss_dssp HHHHHHHHHHHTTSS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHH
Confidence 344557799999999998775
Done!