Query 006202
Match_columns 657
No_of_seqs 93 out of 104
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 19:51:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006202.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006202hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06972 DUF1296: Protein of u 99.9 5.4E-28 1.2E-32 197.0 4.6 59 20-78 1-60 (60)
2 PF02845 CUE: CUE domain; Int 97.5 0.00011 2.5E-09 55.9 4.2 38 25-62 2-40 (42)
3 PF00627 UBA: UBA/TS-N domain; 97.2 0.00045 9.7E-09 51.4 4.2 35 25-60 3-37 (37)
4 smart00546 CUE Domain that may 96.9 0.0018 3.9E-08 49.5 4.6 40 24-63 2-42 (43)
5 smart00165 UBA Ubiquitin assoc 96.7 0.0026 5.6E-08 46.7 4.3 36 25-61 2-37 (37)
6 cd00194 UBA Ubiquitin Associat 96.7 0.003 6.6E-08 46.5 4.5 37 25-62 2-38 (38)
7 PF14555 UBA_4: UBA-like domai 95.5 0.02 4.4E-07 44.0 4.0 38 25-62 1-38 (43)
8 PRK06369 nac nascent polypepti 93.6 0.091 2E-06 49.2 4.3 39 24-62 76-114 (115)
9 TIGR00264 alpha-NAC-related pr 92.9 0.13 2.8E-06 48.4 4.2 37 25-61 79-115 (116)
10 PRK09377 tsf elongation factor 92.5 0.13 2.7E-06 54.7 4.0 38 25-62 6-43 (290)
11 TIGR00601 rad23 UV excision re 92.3 0.15 3.2E-06 55.9 4.3 43 22-65 154-196 (378)
12 CHL00098 tsf elongation factor 91.9 0.17 3.7E-06 51.1 4.0 37 26-62 3-39 (200)
13 TIGR00116 tsf translation elon 91.4 0.2 4.3E-06 53.3 4.0 37 26-62 6-42 (290)
14 PF11547 E3_UbLigase_EDD: E3 u 91.0 0.21 4.6E-06 40.8 2.9 43 18-63 6-49 (53)
15 COG1308 EGD2 Transcription fac 90.9 0.3 6.4E-06 46.4 4.1 37 25-61 85-121 (122)
16 PRK12332 tsf elongation factor 90.4 0.3 6.6E-06 49.3 4.0 37 26-62 6-42 (198)
17 PF03474 DMA: DMRTA motif; In 89.5 0.49 1.1E-05 37.0 3.6 35 27-61 4-39 (39)
18 COG0264 Tsf Translation elonga 88.2 0.53 1.1E-05 50.4 4.0 38 25-62 6-43 (296)
19 PF08938 HBS1_N: HBS1 N-termin 88.0 0.19 4.2E-06 43.4 0.6 39 25-63 29-70 (79)
20 KOG1071 Mitochondrial translat 81.4 1.7 3.7E-05 47.2 4.2 41 23-63 45-85 (340)
21 KOG0943 Predicted ubiquitin-pr 78.6 3.3 7.2E-05 51.6 5.7 48 16-63 179-229 (3015)
22 smart00804 TAP_C C-terminal do 62.3 13 0.00027 31.7 4.1 48 19-72 7-54 (63)
23 PF03943 TAP_C: TAP C-terminal 59.6 7.5 0.00016 31.5 2.2 42 25-72 1-42 (51)
24 KOG0011 Nucleotide excision re 51.2 18 0.00039 39.8 4.1 42 23-65 134-175 (340)
25 PF08006 DUF1700: Protein of u 46.8 17 0.00038 35.3 3.0 46 20-69 17-69 (181)
26 TIGR00601 rad23 UV excision re 46.3 38 0.00082 37.6 5.7 45 18-63 331-375 (378)
27 PF08828 DSX_dimer: Doublesex 45.9 17 0.00038 31.2 2.4 39 25-63 7-48 (62)
28 TIGR00274 N-acetylmuramic acid 43.3 29 0.00063 36.9 4.2 53 19-71 221-277 (291)
29 PRK05441 murQ N-acetylmuramic 42.9 32 0.00068 36.6 4.4 53 19-71 226-282 (299)
30 PF05918 API5: Apoptosis inhib 42.6 8.2 0.00018 44.8 0.0 9 43-51 428-436 (556)
31 PF11626 Rap1_C: TRF2-interact 41.4 27 0.00057 30.8 3.0 32 32-63 4-35 (87)
32 KOG3816 Cell differentiation r 35.1 1.1E+02 0.0024 34.9 7.0 27 18-44 70-96 (526)
33 PF11705 RNA_pol_3_Rpc31: DNA- 29.9 35 0.00075 34.9 2.1 8 64-71 68-75 (233)
34 PF02954 HTH_8: Bacterial regu 29.4 53 0.0012 25.1 2.6 21 40-60 8-28 (42)
35 KOG0011 Nucleotide excision re 28.3 96 0.0021 34.4 5.2 47 19-67 293-339 (340)
36 PRK12570 N-acetylmuramic acid- 26.8 78 0.0017 33.8 4.2 51 18-68 221-275 (296)
37 PHA02616 VP2/VP3; Provisional 23.6 54 0.0012 34.2 2.1 39 39-79 185-229 (259)
38 KOG0010 Ubiquitin-like protein 23.1 1.2E+02 0.0025 35.3 4.8 47 16-62 446-492 (493)
39 KOG2561 Adaptor protein NUB1, 22.6 39 0.00085 38.9 1.0 27 36-62 314-340 (568)
40 KOG0418 Ubiquitin-protein liga 22.5 1.2E+02 0.0027 31.3 4.4 45 18-63 156-200 (200)
No 1
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=99.94 E-value=5.4e-28 Score=197.00 Aligned_cols=59 Identities=86% Similarity=1.268 Sum_probs=57.6
Q ss_pred CCcchHHHHHhhhhccCC-ChHHHHHHHHhcCCCHHHHHHHHhcCCccchhhcccccccc
Q 006202 20 IPAGSRKIVQSLKEIVNC-PESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKSKRDKRKE 78 (657)
Q Consensus 20 ip~~~rk~Vq~lkEi~~~-seeei~~aL~dCn~DpneAv~rLL~~d~f~eVkkKR~kkKE 78 (657)
||+++||+||.||||+|+ ||+|||+||+|||||||||++|||+||+|||||+||+||||
T Consensus 1 IP~~~rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~qD~FheVk~krdkkKE 60 (60)
T PF06972_consen 1 IPAASRKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQDPFHEVKSKRDKKKE 60 (60)
T ss_pred CChHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhcCcHHHHHHhhhhccC
Confidence 899999999999999965 99999999999999999999999999999999999999997
No 2
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=97.53 E-value=0.00011 Score=55.95 Aligned_cols=38 Identities=32% Similarity=0.433 Sum_probs=35.3
Q ss_pred HHHHHhhhhcc-CCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 25 RKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 25 rk~Vq~lkEi~-~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
+..|++|+|+| +++.+.|..+|+.|++|++.||+.||+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 46899999999 999999999999999999999999996
No 3
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=97.24 E-value=0.00045 Score=51.37 Aligned_cols=35 Identities=29% Similarity=0.421 Sum_probs=32.2
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHH
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRL 60 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rL 60 (657)
+++|++|+++ |.+++++..||+.|++|++.|++.|
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 5789999999 9999999999999999999999976
No 4
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=96.85 E-value=0.0018 Score=49.47 Aligned_cols=40 Identities=28% Similarity=0.388 Sum_probs=37.1
Q ss_pred hHHHHHhhhhcc-CCChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 24 SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 24 ~rk~Vq~lkEi~-~~seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
....|.+|+|+| +.+++.|-..|+.|++|++.||+.||+.
T Consensus 2 ~~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 2 NDEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 356899999999 9999999999999999999999999974
No 5
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=96.71 E-value=0.0026 Score=46.71 Aligned_cols=36 Identities=22% Similarity=0.305 Sum_probs=32.8
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHh
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL 61 (657)
+++|++|+++ |.+++++..+|+.|++|++.|++.|+
T Consensus 2 ~~~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 2 EEKIDQLLEM-GFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 5778888887 99999999999999999999999885
No 6
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=96.67 E-value=0.003 Score=46.48 Aligned_cols=37 Identities=24% Similarity=0.312 Sum_probs=33.3
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
+++|++|+++ |.+++++..+|+-|++|++.|++.|++
T Consensus 2 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 2 EEKLEQLLEM-GFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 5678888885 999999999999999999999999874
No 7
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.46 E-value=0.02 Score=44.04 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=33.3
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
+++|.+.++|||++++.....|+.||.|++.||+..+.
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~ 38 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFD 38 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 57899999999999999999999999999999987665
No 8
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=93.60 E-value=0.091 Score=49.24 Aligned_cols=39 Identities=28% Similarity=0.285 Sum_probs=35.4
Q ss_pred hHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 24 ~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
..+.|+.|+|-+|+|+++...||++||+|+-+||-.|-+
T Consensus 76 ~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 76 PEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 467888899999999999999999999999999987754
No 9
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=92.93 E-value=0.13 Score=48.39 Aligned_cols=37 Identities=24% Similarity=0.316 Sum_probs=33.9
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHh
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL 61 (657)
.+.|.-|+|-+|+|+++...||++||+|+-+||-+|-
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 5678888999999999999999999999999998774
No 10
>PRK09377 tsf elongation factor Ts; Provisional
Probab=92.51 E-value=0.13 Score=54.71 Aligned_cols=38 Identities=21% Similarity=0.238 Sum_probs=35.0
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
-+.|+.|+|.||..--||..||.+||+|.+.|++.|-.
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 46799999999999999999999999999999998843
No 11
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.27 E-value=0.15 Score=55.88 Aligned_cols=43 Identities=21% Similarity=0.363 Sum_probs=39.3
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCc
Q 006202 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDP 65 (657)
Q Consensus 22 ~~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~ 65 (657)
...+.+|++|+|+ ||..++|..||+-+.++|+.||++||.+=+
T Consensus 154 ~~~e~~I~~i~eM-Gf~R~qV~~ALRAafNNPdRAVEYL~tGIP 196 (378)
T TIGR00601 154 SERETTIEEIMEM-GYEREEVERALRAAFNNPDRAVEYLLTGIP 196 (378)
T ss_pred hHHHHHHHHHHHh-CCCHHHHHHHHHHHhCCHHHHHHHHHhCCC
Confidence 3668899999998 899999999999999999999999999744
No 12
>CHL00098 tsf elongation factor Ts
Probab=91.89 E-value=0.17 Score=51.11 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=34.2
Q ss_pred HHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 26 k~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
+.|+.|+|.||..--||..||.+|++|.+.|++.|-.
T Consensus 3 ~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~Lr~ 39 (200)
T CHL00098 3 ELVKELRDKTGAGMMDCKKALQEANGDFEKALESLRQ 39 (200)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5799999999999999999999999999999997743
No 13
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=91.43 E-value=0.2 Score=53.25 Aligned_cols=37 Identities=24% Similarity=0.287 Sum_probs=34.3
Q ss_pred HHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 26 k~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
+.|+.|+|.||..--||..||.+|++|.+.|++.|=.
T Consensus 6 ~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRk 42 (290)
T TIGR00116 6 QLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRE 42 (290)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5699999999999999999999999999999998743
No 14
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=91.03 E-value=0.21 Score=40.84 Aligned_cols=43 Identities=30% Similarity=0.461 Sum_probs=32.6
Q ss_pred ccCCcchHHHHHhhhhcc-CCChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 18 SSIPAGSRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 18 ~~ip~~~rk~Vq~lkEi~-~~seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
..||. +.|.+..-+. |++.+-|+.-|+..|.|+|+||+-||+.
T Consensus 6 ~~vPe---dlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR 49 (53)
T PF11547_consen 6 SQVPE---DLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLSR 49 (53)
T ss_dssp GGS-H---HHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred ccCCH---HHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhcc
Confidence 34554 4555555566 9999999999999999999999999974
No 15
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=90.85 E-value=0.3 Score=46.38 Aligned_cols=37 Identities=22% Similarity=0.232 Sum_probs=33.4
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHh
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL 61 (657)
++-|+-+.|=+|.|.+|...||++||+|+-+||=+|.
T Consensus 85 eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 85 EEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 5567777888999999999999999999999999885
No 16
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=90.37 E-value=0.3 Score=49.26 Aligned_cols=37 Identities=27% Similarity=0.311 Sum_probs=34.4
Q ss_pred HHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 26 k~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
+.|+.|+|.||.+--||..||.+|++|.+.|++.|-.
T Consensus 6 ~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~ 42 (198)
T PRK12332 6 KLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLRE 42 (198)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6799999999999999999999999999999997754
No 17
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=89.52 E-value=0.49 Score=37.01 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=30.7
Q ss_pred HHHhhhhcc-CCChHHHHHHHHhcCCCHHHHHHHHh
Q 006202 27 IVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLL 61 (657)
Q Consensus 27 ~Vq~lkEi~-~~seeei~~aL~dCn~DpneAv~rLL 61 (657)
-+..|..+| ++....+-.+|+-|+||+-.||+.+|
T Consensus 4 pidiL~rvFP~~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 4 PIDILTRVFPHQKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred HHHHHHHHCCCCChHHHHHHHHHcCCcHHHHHHHhC
Confidence 356678889 89999999999999999999999765
No 18
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=88.16 E-value=0.53 Score=50.39 Aligned_cols=38 Identities=24% Similarity=0.265 Sum_probs=34.6
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
-..|+.|+|.||..--||..||.||+||.+.||+.|=.
T Consensus 6 a~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 6 AALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 36799999999999999999999999999999997743
No 19
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=88.02 E-value=0.19 Score=43.42 Aligned_cols=39 Identities=26% Similarity=0.401 Sum_probs=31.3
Q ss_pred HHHHHhhhhcc--CC-ChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 25 RKIVQSLKEIV--NC-PESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 25 rk~Vq~lkEi~--~~-seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
+.-+.+||+++ .. ++.+|.-||-.|+.|+++||..||..
T Consensus 29 ~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 29 YSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp CHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred HHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 34567788888 34 89999999999999999999999873
No 20
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=81.43 E-value=1.7 Score=47.17 Aligned_cols=41 Identities=22% Similarity=0.264 Sum_probs=37.9
Q ss_pred chHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 23 GSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 23 ~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
+....|++|+|-||.+-.+|.++|.+||+|...|...|-+.
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~ 85 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKK 85 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 67889999999999999999999999999999999987653
No 21
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=78.64 E-value=3.3 Score=51.56 Aligned_cols=48 Identities=31% Similarity=0.522 Sum_probs=41.3
Q ss_pred CcccCCcc--hHHHHHhhhhcc-CCChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 16 GISSIPAG--SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 16 ~~~~ip~~--~rk~Vq~lkEi~-~~seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
|+-.||+. .++.|.+..-|+ |++.+=|+.-|+..|.|+|+||+-||+.
T Consensus 179 gaPriPAsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLSR 229 (3015)
T KOG0943|consen 179 GAPRIPASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLSR 229 (3015)
T ss_pred CCCcCCcccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhcc
Confidence 45566655 478888888888 9999999999999999999999999976
No 22
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=62.35 E-value=13 Score=31.67 Aligned_cols=48 Identities=21% Similarity=0.297 Sum_probs=40.6
Q ss_pred cCCcchHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCccchhhcc
Q 006202 19 SIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKSK 72 (657)
Q Consensus 19 ~ip~~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~f~eVkkK 72 (657)
.+.+.-+.+|..+.+.||.+.+=....|+++|-|.+.|+. .|.++|++
T Consensus 7 ~~~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~------~F~~lk~~ 54 (63)
T smart00804 7 TLSPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALK------NFTELKSE 54 (63)
T ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHH------HHHHHHhc
Confidence 3556678899999999999999999999999999999998 46666543
No 23
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=59.55 E-value=7.5 Score=31.51 Aligned_cols=42 Identities=24% Similarity=0.284 Sum_probs=33.4
Q ss_pred HHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCccchhhcc
Q 006202 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKSK 72 (657)
Q Consensus 25 rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~f~eVkkK 72 (657)
.++|..+...+|-+.+=...-|++|+-|.+.|+. .|.++|.+
T Consensus 1 q~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~------~F~~l~~~ 42 (51)
T PF03943_consen 1 QEMVQQFSQQTGMNLEWSQKCLEENNWDYERALQ------NFEELKAQ 42 (51)
T ss_dssp HHHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHH------HHHHCCCT
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHH------HHHHHHHc
Confidence 3689999999999999899999999999999998 45555543
No 24
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=51.19 E-value=18 Score=39.78 Aligned_cols=42 Identities=26% Similarity=0.355 Sum_probs=36.7
Q ss_pred chHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCc
Q 006202 23 GSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDP 65 (657)
Q Consensus 23 ~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~ 65 (657)
..+.+|++|+|+ ||..|++..||+-.-..|+.||++||.+-+
T Consensus 134 ~~e~~V~~Im~M-Gy~re~V~~AlRAafNNPeRAVEYLl~GIP 175 (340)
T KOG0011|consen 134 EYEQTVQQIMEM-GYDREEVERALRAAFNNPERAVEYLLNGIP 175 (340)
T ss_pred hhHHHHHHHHHh-CccHHHHHHHHHHhhCChhhhHHHHhcCCc
Confidence 556778887776 799999999999999999999999999753
No 25
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=46.78 E-value=17 Score=35.27 Aligned_cols=46 Identities=26% Similarity=0.388 Sum_probs=34.5
Q ss_pred CC-cchHHHHHhhhhcc------CCChHHHHHHHHhcCCCHHHHHHHHhcCCccchh
Q 006202 20 IP-AGSRKIVQSLKEIV------NCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEV 69 (657)
Q Consensus 20 ip-~~~rk~Vq~lkEi~------~~seeei~~aL~dCn~DpneAv~rLL~~d~f~eV 69 (657)
+| .+.++.++-.+|.+ |.|||||++-| |||.+.++.++.....++.
T Consensus 17 lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~L----G~P~~iA~~i~~~~~i~~~ 69 (181)
T PF08006_consen 17 LPEEEREEILEYYEEYFDDAGEEGKSEEEIIAEL----GSPKEIAREILAEYSIKEE 69 (181)
T ss_pred CCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHc----CCHHHHHHHHHHhhhhhhh
Confidence 44 34677788888877 57999999776 7999999999975444444
No 26
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=46.26 E-value=38 Score=37.64 Aligned_cols=45 Identities=18% Similarity=0.280 Sum_probs=41.0
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 18 ~~ip~~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
..+-+.=++.|+.|+++ |+.+..++-++.-|+-+-+-|+++||++
T Consensus 331 i~lT~eE~~AIeRL~~L-GF~r~~viqaY~ACdKNEelAAn~Lf~~ 375 (378)
T TIGR00601 331 IQVTPEEKEAIERLCAL-GFDRGLVIQAYFACDKNEELAANYLLSQ 375 (378)
T ss_pred cccCHHHHHHHHHHHHc-CCCHHHHHHHHHhcCCcHHHHHHHHHhh
Confidence 45667788999999998 9999999999999999999999999984
No 27
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=45.92 E-value=17 Score=31.19 Aligned_cols=39 Identities=28% Similarity=0.311 Sum_probs=28.3
Q ss_pred HHHHHhhhhccCCChHH---HHHHHHhcCCCHHHHHHHHhcC
Q 006202 25 RKIVQSLKEIVNCPESE---IYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 25 rk~Vq~lkEi~~~seee---i~~aL~dCn~DpneAv~rLL~~ 63 (657)
-+--|.|.|-|+.+=|= .|++|++.+.|++||..||-++
T Consensus 7 l~~cqkLlEkf~YpWEmmpLmyVILK~A~~D~eeA~rrI~E~ 48 (62)
T PF08828_consen 7 LERCQKLLEKFRYPWEMMPLMYVILKYADADVEEASRRIDEA 48 (62)
T ss_dssp HHHHHHHHHHTT--GGGHHHHHHHHHHTTT-HHHHHHHHHH-
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 34456777888766554 5899999999999999999875
No 28
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=43.35 E-value=29 Score=36.88 Aligned_cols=53 Identities=19% Similarity=0.263 Sum_probs=40.4
Q ss_pred cCCcchHHH----HHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCccchhhc
Q 006202 19 SIPAGSRKI----VQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (657)
Q Consensus 19 ~ip~~~rk~----Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~f~eVkk 71 (657)
.+-+.-.|. +.-|++++|+++++...+|.+|++.+--||=.++..-.+.+-++
T Consensus 221 d~~~~N~kl~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~~~~~~~a~~ 277 (291)
T TIGR00274 221 DVQASNEKLKARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMILSTLSASEAKV 277 (291)
T ss_pred eeecccHHHHHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 344444444 45578888999999999999999999999987777656655544
No 29
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=42.92 E-value=32 Score=36.63 Aligned_cols=53 Identities=21% Similarity=0.199 Sum_probs=40.3
Q ss_pred cCCcchHHHH----HhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCccchhhc
Q 006202 19 SIPAGSRKIV----QSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (657)
Q Consensus 19 ~ip~~~rk~V----q~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~f~eVkk 71 (657)
.+-++-.|.+ .-|++++|+++++...+|.+|++++-.||=.++.+-.+.+-++
T Consensus 226 d~~~~n~kl~~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~~~~~~a~~ 282 (299)
T PRK05441 226 DVKATNEKLVDRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMILTGLDAAEAKA 282 (299)
T ss_pred HhcCCHHHHHHHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 3444444444 4578888999999999999999999999988887655555544
No 30
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=42.61 E-value=8.2 Score=44.78 Aligned_cols=9 Identities=33% Similarity=0.261 Sum_probs=6.0
Q ss_pred HHHHHhcCC
Q 006202 43 YAMLKECNM 51 (657)
Q Consensus 43 ~~aL~dCn~ 51 (657)
..+|+-|+.
T Consensus 428 ~~aLkt~~N 436 (556)
T PF05918_consen 428 VTALKTTNN 436 (556)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHhh
Confidence 367777764
No 31
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=41.37 E-value=27 Score=30.77 Aligned_cols=32 Identities=19% Similarity=0.087 Sum_probs=27.0
Q ss_pred hhccCCChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 32 KEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 32 kEi~~~seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
.+-+|.+++.|..||.-|.||+..|...+|..
T Consensus 4 ~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 4 YEELGYSREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp HHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred HHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 44569999999999999999999999977764
No 32
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=35.05 E-value=1.1e+02 Score=34.89 Aligned_cols=27 Identities=11% Similarity=-0.039 Sum_probs=12.6
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHH
Q 006202 18 SSIPAGSRKIVQSLKEIVNCPESEIYA 44 (657)
Q Consensus 18 ~~ip~~~rk~Vq~lkEi~~~seeei~~ 44 (657)
+..|+..-.+...+.|..-.+-.+|.+
T Consensus 70 ~~~~aG~~~~~Da~~~~~~~t~~~C~~ 96 (526)
T KOG3816|consen 70 AAAAAGAAAAGDAKNEAPCATPLICSF 96 (526)
T ss_pred hcccccchhcccccccccccChhhceE
Confidence 334444444455555554444444443
No 33
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=29.95 E-value=35 Score=34.92 Aligned_cols=8 Identities=13% Similarity=0.372 Sum_probs=4.4
Q ss_pred Cccchhhc
Q 006202 64 DPFHEVKS 71 (657)
Q Consensus 64 d~f~eVkk 71 (657)
.+|..+.+
T Consensus 68 sPyy~~~~ 75 (233)
T PF11705_consen 68 SPYYTESR 75 (233)
T ss_pred CCCccccc
Confidence 46666644
No 34
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=29.41 E-value=53 Score=25.10 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHH
Q 006202 40 SEIYAMLKECNMDPNEAVNRL 60 (657)
Q Consensus 40 eei~~aL~dCn~DpneAv~rL 60 (657)
+-|..+|+.|+++..+|...|
T Consensus 8 ~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 8 QLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 457889999999999999866
No 35
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=28.34 E-value=96 Score=34.38 Aligned_cols=47 Identities=19% Similarity=0.418 Sum_probs=37.7
Q ss_pred cCCcchHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCccc
Q 006202 19 SIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFH 67 (657)
Q Consensus 19 ~ip~~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~f~ 67 (657)
.+-+.-++-|..|+.+ |..+.=++-|+--|+=+-+-|+++||++. |.
T Consensus 293 ~vtpee~eAIeRL~al-GF~ralViqayfACdKNEelAAN~Ll~~~-f~ 339 (340)
T KOG0011|consen 293 QVTPEEKEAIERLEAL-GFPRALVIQAYFACDKNEELAANYLLSHS-FE 339 (340)
T ss_pred ecCHHHHHHHHHHHHh-CCcHHHHHHHHHhcCccHHHHHHHHHhhc-cC
Confidence 3445667778887654 77888888999999999999999999965 64
No 36
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=26.77 E-value=78 Score=33.78 Aligned_cols=51 Identities=24% Similarity=0.350 Sum_probs=37.2
Q ss_pred ccCCcchHHH----HHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcCCccch
Q 006202 18 SSIPAGSRKI----VQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHE 68 (657)
Q Consensus 18 ~~ip~~~rk~----Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~d~f~e 68 (657)
+.+-++-.|. +.-|++++|+++++...+|++|++.+--||=.++.+-+..+
T Consensus 221 vd~~~~n~kl~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~~~~~~~ 275 (296)
T PRK12570 221 VDVKATNEKLVARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMILTGMDVEQ 275 (296)
T ss_pred EEeecchHHHHHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHhCCCHHH
Confidence 3444454444 44578888999999999999999999888876666433333
No 37
>PHA02616 VP2/VP3; Provisional
Probab=23.58 E-value=54 Score=34.17 Aligned_cols=39 Identities=38% Similarity=0.382 Sum_probs=26.2
Q ss_pred hHHHHHHHHhcCCCHHH----HHHHHhcCCccchh--hccccccccc
Q 006202 39 ESEIYAMLKECNMDPNE----AVNRLLSQDPFHEV--KSKRDKRKES 79 (657)
Q Consensus 39 eeei~~aL~dCn~Dpne----Av~rLL~~d~f~eV--kkKR~kkKE~ 79 (657)
.+=|+++|+|-|-|.++ ||.|- ||-.|-| .||+.+.|+.
T Consensus 185 PdWiLyVLEeLn~di~kiptq~vkrk--q~~lh~~~~~kk~~~skKs 229 (259)
T PHA02616 185 PDWILYVLEELNKDIYKIPTQAVKRK--QDELHPVSPTKKAALSKKS 229 (259)
T ss_pred hHHHHHHHHHHHHHHhhcchhhhhhh--ccccCcCCchhhHHHHhhc
Confidence 34578888888888776 77665 7888887 3444444443
No 38
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=23.15 E-value=1.2e+02 Score=35.27 Aligned_cols=47 Identities=19% Similarity=0.160 Sum_probs=42.1
Q ss_pred CcccCCcchHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 16 GISSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 16 ~~~~ip~~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
..+.+...+..-+++|.++.=...|+-+.||.-.++|++.||+|||.
T Consensus 446 ~~~~pe~r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~ 492 (493)
T KOG0010|consen 446 QTVPPEERYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLG 492 (493)
T ss_pred CCCCchHHHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence 45677788889999999988788899999999999999999999985
No 39
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=22.57 E-value=39 Score=38.87 Aligned_cols=27 Identities=30% Similarity=0.448 Sum_probs=23.2
Q ss_pred CCChHHHHHHHHhcCCCHHHHHHHHhc
Q 006202 36 NCPESEIYAMLKECNMDPNEAVNRLLS 62 (657)
Q Consensus 36 ~~seeei~~aL~dCn~DpneAv~rLL~ 62 (657)
|.-+-|---+|+-|++|++.||++|.+
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~e 340 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIE 340 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHH
Confidence 555666677999999999999999987
No 40
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.53 E-value=1.2e+02 Score=31.31 Aligned_cols=45 Identities=27% Similarity=0.252 Sum_probs=38.9
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHHhcCCCHHHHHHHHhcC
Q 006202 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (657)
Q Consensus 18 ~~ip~~~rk~Vq~lkEi~~~seeei~~aL~dCn~DpneAv~rLL~~ 63 (657)
........++|..|+|+ |.++++++.+|.--+.+.++|.+-||++
T Consensus 156 ~~~~~~~~~~v~~l~~m-Gf~~~~~i~~L~~~~w~~~~a~~~~~s~ 200 (200)
T KOG0418|consen 156 LPDDPWDKKKVDSLIEM-GFSELEAILVLSGSDWNLADATEQLLSG 200 (200)
T ss_pred CCCCchhHHHHHHHHHh-cccHHHHHHHhhccccchhhhhHhhccC
Confidence 44567889999998875 8899999999999999999999988863
Done!