Query 003043
Match_columns 854
No_of_seqs 119 out of 136
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 15:54:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003043.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003043hhsearch_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 7.4E-26 1.6E-30 189.0 3.5 59 20-78 1-60 (60)
2 PF02845 CUE: CUE domain; Int 97.7 3.2E-05 7E-10 60.9 4.1 38 25-62 2-40 (42)
3 smart00546 CUE Domain that may 97.0 0.00092 2E-08 52.8 4.4 39 24-62 2-41 (43)
4 PF00627 UBA: UBA/TS-N domain; 96.9 0.0012 2.6E-08 50.8 4.2 35 25-60 3-37 (37)
5 cd00194 UBA Ubiquitin Associat 96.6 0.003 6.4E-08 48.2 4.4 37 25-62 2-38 (38)
6 smart00165 UBA Ubiquitin assoc 96.6 0.0029 6.3E-08 48.1 4.3 36 25-61 2-37 (37)
7 PF14555 UBA_4: UBA-like domai 94.5 0.052 1.1E-06 43.2 3.9 38 25-62 1-38 (43)
8 PRK06369 nac nascent polypepti 92.9 0.13 2.9E-06 49.7 4.4 39 24-62 76-114 (115)
9 TIGR00264 alpha-NAC-related pr 92.8 0.13 2.9E-06 49.8 4.3 39 24-62 78-116 (116)
10 PRK09377 tsf elongation factor 92.1 0.14 3.1E-06 56.2 3.9 38 25-62 6-43 (290)
11 COG1308 EGD2 Transcription fac 92.0 0.19 4.1E-06 49.0 4.2 39 24-62 84-122 (122)
12 PF11547 E3_UbLigase_EDD: E3 u 91.4 0.27 5.9E-06 41.2 3.9 39 25-63 10-49 (53)
13 TIGR00601 rad23 UV excision re 90.1 0.29 6.3E-06 55.5 4.1 41 22-63 154-194 (378)
14 PF08938 HBS1_N: HBS1 N-termin 89.9 0.11 2.3E-06 46.6 0.4 38 25-62 29-69 (79)
15 CHL00098 tsf elongation factor 89.5 0.26 5.6E-06 51.6 2.8 37 26-62 3-39 (200)
16 TIGR00116 tsf translation elon 88.5 0.37 7.9E-06 53.0 3.2 38 25-62 5-42 (290)
17 PRK12332 tsf elongation factor 87.8 0.4 8.6E-06 50.1 2.8 37 26-62 6-42 (198)
18 PF03474 DMA: DMRTA motif; In 87.6 0.62 1.4E-05 37.5 3.2 36 26-61 3-39 (39)
19 COG0264 Tsf Translation elonga 84.8 0.97 2.1E-05 49.9 4.0 38 25-62 6-43 (296)
20 KOG1071 Mitochondrial translat 80.8 1 2.2E-05 50.3 2.2 41 23-63 45-85 (340)
21 KOG0943 Predicted ubiquitin-pr 77.4 3.8 8.2E-05 52.3 5.7 48 16-63 179-229 (3015)
22 KOG0011 Nucleotide excision re 71.7 4.1 9E-05 45.8 3.9 41 22-63 133-173 (340)
23 TIGR00601 rad23 UV excision re 57.3 18 0.00039 41.5 5.6 45 18-63 331-375 (378)
24 KOG0011 Nucleotide excision re 54.4 19 0.00042 40.7 5.1 49 17-67 291-339 (340)
25 TIGR00274 N-acetylmuramic acid 45.3 17 0.00037 40.1 2.9 48 24-71 230-277 (291)
26 PRK05441 murQ N-acetylmuramic 44.9 19 0.00042 39.6 3.3 47 25-71 236-282 (299)
27 PF08006 DUF1700: Protein of u 42.4 18 0.00039 36.5 2.4 40 20-63 17-63 (181)
28 KOG0418 Ubiquitin-protein liga 38.3 45 0.00097 35.4 4.5 44 18-62 156-199 (200)
29 PF08828 DSX_dimer: Doublesex 33.9 31 0.00068 30.5 2.2 39 25-63 7-48 (62)
30 PRK12570 N-acetylmuramic acid- 33.5 46 0.00099 36.8 3.9 40 24-63 231-270 (296)
31 KOG3816 Cell differentiation r 31.8 83 0.0018 36.7 5.6 8 65-72 171-178 (526)
32 PF11626 Rap1_C: TRF2-interact 31.4 43 0.00092 30.6 2.7 31 33-63 5-35 (87)
33 PF03943 TAP_C: TAP C-terminal 27.9 43 0.00092 28.1 2.0 37 25-61 1-37 (51)
34 COG2103 Predicted sugar phosph 27.5 52 0.0011 36.8 3.0 55 17-71 222-280 (298)
35 KOG0010 Ubiquitin-like protein 26.5 76 0.0016 37.8 4.3 47 16-62 446-492 (493)
36 KOG2561 Adaptor protein NUB1, 25.1 35 0.00076 40.3 1.3 27 36-62 314-340 (568)
37 COG5222 Uncharacterized conser 24.6 73 0.0016 36.0 3.5 35 621-663 378-412 (427)
38 PHA02616 VP2/VP3; Provisional 24.2 48 0.001 35.5 2.0 39 39-79 185-229 (259)
39 PF02954 HTH_8: Bacterial regu 23.4 72 0.0016 25.3 2.4 21 40-60 8-28 (42)
40 KOG0917 Uncharacterized conser 23.2 7.4E+02 0.016 28.2 10.6 36 621-656 181-217 (338)
41 smart00804 TAP_C C-terminal do 21.5 1.6E+02 0.0035 26.0 4.3 43 19-61 7-49 (63)
42 PF11705 RNA_pol_3_Rpc31: DNA- 20.4 66 0.0014 34.2 2.1 9 1-9 1-9 (233)
43 PF07934 OGG_N: 8-oxoguanine D 20.1 47 0.001 31.3 0.9 47 22-68 63-116 (117)
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=99.92 E-value=7.4e-26 Score=188.97 Aligned_cols=59 Identities=86% Similarity=1.268 Sum_probs=57.4
Q ss_pred CCcchHHHHHhhhhccCC-ChHHHHHHHhhcCCCHHHHHHhhhcCCCcceeecccccccc
Q 003043 20 IPAGSRKIVQSLKEIVNC-PESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKSKRDKRKE 78 (854)
Q Consensus 20 ip~~~rk~V~~ikEi~~~-seedi~~aL~ecn~D~n~av~rLl~q~~~~EVkkKr~kkKe 78 (854)
||+++||+||.||||+++ ||+|||+||+|||||||||++|||+||+|||||+||+||||
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 899999999999999955 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=97.75 E-value=3.2e-05 Score=60.93 Aligned_cols=38 Identities=32% Similarity=0.433 Sum_probs=35.5
Q ss_pred HHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 25 RKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 25 rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
+++|+.||||| +|+++.|..+|++|++|++.||+.||+
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 57899999999 999999999999999999999999997
No 3
>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=97.03 E-value=0.00092 Score=52.84 Aligned_cols=39 Identities=28% Similarity=0.406 Sum_probs=36.9
Q ss_pred hHHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 24 SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 24 ~rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
..+.|..|+|+| +.+++.|..+|++|++|++.||+.||+
T Consensus 2 ~~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 2 NDEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 357899999999 999999999999999999999999997
No 4
>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=96.94 E-value=0.0012 Score=50.76 Aligned_cols=35 Identities=29% Similarity=0.421 Sum_probs=32.0
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhh
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRL 60 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rL 60 (854)
+++|++|+++ |.+++++..||+.|++|++.||+.|
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 6889999999 9999999999999999999999865
No 5
>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=96.65 E-value=0.003 Score=48.21 Aligned_cols=37 Identities=24% Similarity=0.312 Sum_probs=34.1
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
+++|++|.++ |.+++++..||+-|++|++.|++.|++
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 5789999887 999999999999999999999998874
No 6
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=96.64 E-value=0.0029 Score=48.08 Aligned_cols=36 Identities=22% Similarity=0.305 Sum_probs=33.5
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhh
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl 61 (854)
+++|++|+++ |.+++++..||+.|++|++.|++.|+
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 6789999998 99999999999999999999999875
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=94.46 E-value=0.052 Score=43.22 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=33.3
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
+++|.+.++|+|++++.....|+.|+.|++.||+..+.
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=92.88 E-value=0.13 Score=49.67 Aligned_cols=39 Identities=28% Similarity=0.285 Sum_probs=35.4
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
..+.|..|+|-+++|+++...||++||+|+-+||-.|-+
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=92.83 E-value=0.13 Score=49.75 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=34.8
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
..+.|..|+|-+++|+++-..||++||+|+-+||-+|-+
T Consensus 78 ~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~~ 116 (116)
T TIGR00264 78 TEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLEE 116 (116)
T ss_pred CHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhhC
Confidence 357788899999999999999999999999999987753
No 10
>PRK09377 tsf elongation factor Ts; Provisional
Probab=92.09 E-value=0.14 Score=56.19 Aligned_cols=38 Identities=21% Similarity=0.238 Sum_probs=35.2
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
-+.|+.|||.||..--||..||.|||+|.+.|++.|-+
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 46899999999999999999999999999999998755
No 11
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=91.99 E-value=0.19 Score=49.02 Aligned_cols=39 Identities=23% Similarity=0.240 Sum_probs=34.2
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
.++-|+.|.|=++.|++|...||+|||+|+-+||-+|.+
T Consensus 84 ~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~~ 122 (122)
T COG1308 84 SEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLTE 122 (122)
T ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhcC
Confidence 356677788888999999999999999999999999863
No 12
>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=91.44 E-value=0.27 Score=41.21 Aligned_cols=39 Identities=28% Similarity=0.399 Sum_probs=31.2
Q ss_pred HHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 25 RKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 25 rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
++.|.+...++ |.|.+-|+.-|+-+|.|+|+||+-||+.
T Consensus 10 edlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsR 49 (53)
T PF11547_consen 10 EDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLSR 49 (53)
T ss_dssp HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhcc
Confidence 45566665567 9999999999999999999999999973
No 13
>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=90.15 E-value=0.29 Score=55.51 Aligned_cols=41 Identities=20% Similarity=0.350 Sum_probs=38.4
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
...+.+|+.|.|| ||.+++|..||+-+.++|+.||+.||.+
T Consensus 154 ~~~e~~I~~i~eM-Gf~R~qV~~ALRAafNNPdRAVEYL~tG 194 (378)
T TIGR00601 154 SERETTIEEIMEM-GYEREEVERALRAAFNNPDRAVEYLLTG 194 (378)
T ss_pred hHHHHHHHHHHHh-CCCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence 3668899999999 9999999999999999999999999995
No 14
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=89.95 E-value=0.11 Score=46.58 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=31.0
Q ss_pred HHHHHhhhhcc--CC-ChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 25 RKIVQSLKEIV--NC-PESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 25 rk~V~~ikEi~--~~-seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
+.-+..||+++ .. ++.+|.-||-.|++|++.||..||+
T Consensus 29 ~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 29 YSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp CHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 34566788888 35 8999999999999999999999998
No 15
>CHL00098 tsf elongation factor Ts
Probab=89.48 E-value=0.26 Score=51.56 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=34.4
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
+.|+.|||.||..--||..||.+|++|.+.|++.|-+
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 5799999999999999999999999999999997755
No 16
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=88.46 E-value=0.37 Score=53.05 Aligned_cols=38 Identities=24% Similarity=0.274 Sum_probs=34.9
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
-+.|+.|||.||..--||..||.||++|.+.|++.|-+
T Consensus 5 a~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRk 42 (290)
T TIGR00116 5 AQLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRE 42 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 35799999999999999999999999999999997755
No 17
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=87.75 E-value=0.4 Score=50.12 Aligned_cols=37 Identities=27% Similarity=0.311 Sum_probs=34.5
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
+.|+.|||.+|..--||..||.+|++|.+.|+..|-+
T Consensus 6 ~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~ 42 (198)
T PRK12332 6 KLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLRE 42 (198)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6799999999999999999999999999999997765
No 18
>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=87.62 E-value=0.62 Score=37.47 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=31.2
Q ss_pred HHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHhhh
Q 003043 26 KIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLL 61 (854)
Q Consensus 26 k~V~~ikEi~-~~seedi~~aL~ecn~D~n~av~rLl 61 (854)
.-+..|..+| ......+=.+|+-|+||+-.||+.+|
T Consensus 3 ~pidiL~rvFP~~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 3 SPIDILTRVFPHQKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred CHHHHHHHHCCCCChHHHHHHHHHcCCcHHHHHHHhC
Confidence 3466788899 88899999999999999999998765
No 19
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=84.84 E-value=0.97 Score=49.94 Aligned_cols=38 Identities=24% Similarity=0.265 Sum_probs=34.5
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
-+.|+.|||.||..=-||..||.||++|.+.||+.|=+
T Consensus 6 a~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 6 AALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 36799999999999999999999999999999997654
No 20
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=80.78 E-value=1 Score=50.33 Aligned_cols=41 Identities=22% Similarity=0.264 Sum_probs=38.3
Q ss_pred chHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 23 GSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 23 ~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
+....|++|||-||.+-.+|.++|.|||+|...|...|-+.
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 67899999999999999999999999999999999987764
No 21
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=77.40 E-value=3.8 Score=52.34 Aligned_cols=48 Identities=31% Similarity=0.522 Sum_probs=41.5
Q ss_pred CcccCCcc--hHHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 16 GISSIPAG--SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 16 ~~~~ip~~--~rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
++-.||+. .++.|.+..-|+ |.|.+-|+.-|+.++.|+|+||+.||+.
T Consensus 179 gaPriPAsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLSR 229 (3015)
T KOG0943|consen 179 GAPRIPASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLSR 229 (3015)
T ss_pred CCCcCCcccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhcc
Confidence 45556653 588899988888 9999999999999999999999999976
No 22
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=71.65 E-value=4.1 Score=45.80 Aligned_cols=41 Identities=24% Similarity=0.341 Sum_probs=37.4
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
...+.+|++|.|| ||..|++.+||+-.-..|+.||+.||.+
T Consensus 133 ~~~e~~V~~Im~M-Gy~re~V~~AlRAafNNPeRAVEYLl~G 173 (340)
T KOG0011|consen 133 SEYEQTVQQIMEM-GYDREEVERALRAAFNNPERAVEYLLNG 173 (340)
T ss_pred chhHHHHHHHHHh-CccHHHHHHHHHHhhCChhhhHHHHhcC
Confidence 3567788999888 9999999999999999999999999994
No 23
>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=57.30 E-value=18 Score=41.51 Aligned_cols=45 Identities=18% Similarity=0.280 Sum_probs=41.3
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 18 ~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
..|-..-|+.|+.|+++ ||.+..++-|..-|+-+.+.|++.||++
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 56667889999999988 9999999999999999999999999984
No 24
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=54.41 E-value=19 Score=40.73 Aligned_cols=49 Identities=18% Similarity=0.376 Sum_probs=41.1
Q ss_pred cccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcCCCcc
Q 003043 17 ISSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFH 67 (854)
Q Consensus 17 ~~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q~~~~ 67 (854)
.+.+-+.-++-|..||.+ |..+.=++-|.--|+=+.+.|++.||++. |+
T Consensus 291 ~I~vtpee~eAIeRL~al-GF~ralViqayfACdKNEelAAN~Ll~~~-f~ 339 (340)
T KOG0011|consen 291 QIQVTPEEKEAIERLEAL-GFPRALVIQAYFACDKNEELAANYLLSHS-FE 339 (340)
T ss_pred eEecCHHHHHHHHHHHHh-CCcHHHHHHHHHhcCccHHHHHHHHHhhc-cC
Confidence 344556778889999776 99888899999999999999999999954 54
No 25
>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=45.32 E-value=17 Score=40.09 Aligned_cols=48 Identities=17% Similarity=0.206 Sum_probs=38.9
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcCCCcceeec
Q 003043 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (854)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q~~~~EVkk 71 (854)
+++-+..|.+++|+++++...+|.+|++++-.||--++..-.+.|-++
T Consensus 230 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~~~~~~~a~~ 277 (291)
T TIGR00274 230 KARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMILSTLSASEAKV 277 (291)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 455567788899999999999999999999999987777445555444
No 26
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=44.89 E-value=19 Score=39.63 Aligned_cols=47 Identities=19% Similarity=0.153 Sum_probs=37.6
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcCCCcceeec
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q~~~~EVkk 71 (854)
++-+..|.+++|+++++...+|++|++++-.||-.++..-.+.+-++
T Consensus 236 ~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~~~~~~a~~ 282 (299)
T PRK05441 236 DRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMILTGLDAAEAKA 282 (299)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 34456788888999999999999999999999998877445554443
No 27
>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=42.36 E-value=18 Score=36.55 Aligned_cols=40 Identities=28% Similarity=0.439 Sum_probs=32.5
Q ss_pred CCc-chHHHHHhhhhcc------CCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 20 IPA-GSRKIVQSLKEIV------NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 20 ip~-~~rk~V~~ikEi~------~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
+|. +.++.++-.+|.| |.+||||++-| +||.+.+..++..
T Consensus 17 lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~L----G~P~~iA~~i~~~ 63 (181)
T PF08006_consen 17 LPEEEREEILEYYEEYFDDAGEEGKSEEEIIAEL----GSPKEIAREILAE 63 (181)
T ss_pred CCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHc----CCHHHHHHHHHHh
Confidence 554 5777888888877 46899999877 8999999999873
No 28
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.32 E-value=45 Score=35.35 Aligned_cols=44 Identities=27% Similarity=0.265 Sum_probs=39.0
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 18 ~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
...-....++|..|+|+ |.++++++.+|.--+-+.++|.+-||+
T Consensus 156 ~~~~~~~~~~v~~l~~m-Gf~~~~~i~~L~~~~w~~~~a~~~~~s 199 (200)
T KOG0418|consen 156 LPDDPWDKKKVDSLIEM-GFSELEAILVLSGSDWNLADATEQLLS 199 (200)
T ss_pred CCCCchhHHHHHHHHHh-cccHHHHHHHhhccccchhhhhHhhcc
Confidence 34446788999999998 999999999999999999999998886
No 29
>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=33.85 E-value=31 Score=30.53 Aligned_cols=39 Identities=28% Similarity=0.304 Sum_probs=28.1
Q ss_pred HHHHHhhhhccCCChH---HHHHHHhhcCCCHHHHHHhhhcC
Q 003043 25 RKIVQSLKEIVNCPES---EIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 25 rk~V~~ikEi~~~see---di~~aL~ecn~D~n~av~rLl~q 63 (854)
-|--+.|.|-|+.+=| =.|.+|++.+.|++||..||-+.
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 3455678888865533 46889999999999999999884
No 30
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=33.47 E-value=46 Score=36.82 Aligned_cols=40 Identities=25% Similarity=0.372 Sum_probs=33.9
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
+++-+..|.+++|+++++.-.+|++|++++-.||--++..
T Consensus 231 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~~ 270 (296)
T PRK12570 231 VARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMILTG 270 (296)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHhC
Confidence 4455677888899999999999999999999999866653
No 31
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=31.85 E-value=83 Score=36.74 Aligned_cols=8 Identities=25% Similarity=0.310 Sum_probs=5.3
Q ss_pred Ccceeecc
Q 003043 65 PFHEVKSK 72 (854)
Q Consensus 65 ~~~EVkkK 72 (854)
-|-.||+-
T Consensus 171 DW~~~~~~ 178 (526)
T KOG3816|consen 171 DWYQVKRM 178 (526)
T ss_pred CccCcccc
Confidence 37777763
No 32
>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=31.40 E-value=43 Score=30.59 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=25.7
Q ss_pred hccCCChHHHHHHHhhcCCCHHHHHHhhhcC
Q 003043 33 EIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (854)
Q Consensus 33 Ei~~~seedi~~aL~ecn~D~n~av~rLl~q 63 (854)
+-+|.+++.|..||.-|.||+..|...||..
T Consensus 5 ~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 5 EELGYSREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp HHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred HHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 3349999999999999999999999966653
No 33
>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=27.94 E-value=43 Score=28.14 Aligned_cols=37 Identities=19% Similarity=0.159 Sum_probs=29.6
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhh
Q 003043 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (854)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl 61 (854)
.++|..+...+|...+=....|+|++-|.+.|+....
T Consensus 1 q~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 1 QEMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFE 37 (51)
T ss_dssp HHHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3688899999988888888899999999999998443
No 34
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=27.46 E-value=52 Score=36.75 Aligned_cols=55 Identities=25% Similarity=0.323 Sum_probs=41.3
Q ss_pred cccCCcchHHH----HHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhcCCCcceeec
Q 003043 17 ISSIPAGSRKI----VQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (854)
Q Consensus 17 ~~~ip~~~rk~----V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~q~~~~EVkk 71 (854)
-+.+-++.+|. +..|+|+++++.|+--++|++|++++-.||--++..-.-+|-++
T Consensus 222 MVDv~atN~KL~dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~~~~~~a~~A~~ 280 (298)
T COG2103 222 MVDVKATNEKLRDRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVMLLTGLSAEEAKR 280 (298)
T ss_pred EEEeecchHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHHHhCCCHHHHHH
Confidence 34555666665 45677888999999999999999999999987776444444433
No 35
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=26.47 E-value=76 Score=37.85 Aligned_cols=47 Identities=19% Similarity=0.160 Sum_probs=41.4
Q ss_pred CcccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 16 GISSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 16 ~~~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
..+.++..+..-++++.++.=...|+-+.||.-+++|++.||+|||.
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 56677788888999999986567899999999999999999999985
No 36
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=25.11 E-value=35 Score=40.31 Aligned_cols=27 Identities=30% Similarity=0.448 Sum_probs=24.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHhhhc
Q 003043 36 NCPESEIYAMLKECNMDPNEAVNRLLS 62 (854)
Q Consensus 36 ~~seedi~~aL~ecn~D~n~av~rLl~ 62 (854)
|.-+-|---||+-|++|++.||++|++
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~e 340 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIE 340 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHH
Confidence 566778888999999999999999998
No 37
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=24.60 E-value=73 Score=36.04 Aligned_cols=35 Identities=26% Similarity=0.456 Sum_probs=20.3
Q ss_pred CCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCC
Q 003043 621 MPGASVATGPALPPHLAVHPYSQPTLPLGHFANMIGYPFLPQS 663 (854)
Q Consensus 621 ~ps~~i~~~~~~pQ~l~~hpy~Qp~lp~~hy~N~~~Ypylp~~ 663 (854)
.|..--++++|+|.++ ||+- +| +|+ |||.|+|||-
T Consensus 378 ~pa~~~~~~~p~p~~p--~~~g---~p--pfp-m~plp~mpp~ 412 (427)
T COG5222 378 EPAFKSAMAIPMPSMP--HVQG---FP--PFP-MMPLPQMPPM 412 (427)
T ss_pred cchhhhcCCCCCCCCC--ccCC---CC--CCC-CCCCCCCCcc
Confidence 3444456677788775 4333 22 365 8887775544
No 38
>PHA02616 VP2/VP3; Provisional
Probab=24.21 E-value=48 Score=35.45 Aligned_cols=39 Identities=38% Similarity=0.382 Sum_probs=26.0
Q ss_pred hHHHHHHHhhcCCCHHH----HHHhhhcCCCcceee--ccccccccc
Q 003043 39 ESEIYAMLKECNMDPNE----AVNRLLSQDPFHEVK--SKRDKRKES 79 (854)
Q Consensus 39 eedi~~aL~ecn~D~n~----av~rLl~q~~~~EVk--kKr~kkKe~ 79 (854)
.+=|+++|+|.|-|.++ ||.|- ||-.|-|. ||+.+.|+.
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 34588999998888877 55553 67788776 344444443
No 39
>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=23.42 E-value=72 Score=25.27 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=17.0
Q ss_pred HHHHHHHhhcCCCHHHHHHhh
Q 003043 40 SEIYAMLKECNMDPNEAVNRL 60 (854)
Q Consensus 40 edi~~aL~ecn~D~n~av~rL 60 (854)
+-|..+|+.|+++..+|...|
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 457889999999999998755
No 40
>KOG0917 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.22 E-value=7.4e+02 Score=28.21 Aligned_cols=36 Identities=28% Similarity=0.561 Sum_probs=23.7
Q ss_pred CCCCcCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCcc
Q 003043 621 MPGASVATGPALPPHLAVHPYSQPTLPLGHF-ANMIG 656 (854)
Q Consensus 621 ~ps~~i~~~~~~pQ~l~~hpy~Qp~lp~~hy-~N~~~ 656 (854)
+|+.+-+++++-|+-....||.|+.+|-++| .+||.
T Consensus 181 ~P~~tGp~~~syp~Py~p~p~~q~p~p~~p~~~~yiS 217 (338)
T KOG0917|consen 181 LPTQTGPTQPSYPSPYDPSPYHQDPMPSGPYTGIYIS 217 (338)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceee
Confidence 4444444555566666667788888888888 77774
No 41
>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=21.48 E-value=1.6e+02 Score=25.99 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=36.8
Q ss_pred cCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHhhh
Q 003043 19 SIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (854)
Q Consensus 19 ~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~av~rLl 61 (854)
.+.+.-+.+|..+.+.++..-+=....|++++-|.+.|+....
T Consensus 7 ~~~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~ 49 (63)
T smart00804 7 TLSPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFT 49 (63)
T ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3445668899999999999999999999999999999997433
No 42
>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=20.41 E-value=66 Score=34.22 Aligned_cols=9 Identities=78% Similarity=1.523 Sum_probs=4.5
Q ss_pred CCCCCCCCC
Q 003043 1 MSGKGGGGG 9 (854)
Q Consensus 1 m~~~~~g~~ 9 (854)
|||-|||||
T Consensus 1 MSgRGggrg 9 (233)
T PF11705_consen 1 MSGRGGGRG 9 (233)
T ss_pred CCCCCCCCC
Confidence 885333333
No 43
>PF07934 OGG_N: 8-oxoguanine DNA glycosylase, N-terminal domain; InterPro: IPR012904 The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (3.2.2.23 from EC) and DNA lyase activity (4.2.99.18 from EC) []. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket []. ; GO: 0003684 damaged DNA binding, 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006289 nucleotide-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 1N39_A 1LWV_A 1YQM_A 2NOL_A 1YQL_A 1LWY_A ....
Probab=20.07 E-value=47 Score=31.28 Aligned_cols=47 Identities=21% Similarity=0.408 Sum_probs=29.8
Q ss_pred cchHHHHHhhhhcc--CCChHHHHHHHhhcCCCHHHHHH-----hhhcCCCcce
Q 003043 22 AGSRKIVQSLKEIV--NCPESEIYAMLKECNMDPNEAVN-----RLLSQDPFHE 68 (854)
Q Consensus 22 ~~~rk~V~~ikEi~--~~seedi~~aL~ecn~D~n~av~-----rLl~q~~~~E 68 (854)
...++....|++.| +...++|+..+.+.+--...|+. |||.||+|+.
T Consensus 63 ~~~~~~~~~l~~YF~Ld~dl~~l~~~~~~~D~~l~~~~~~~~GlRiLrQdp~E~ 116 (117)
T PF07934_consen 63 SSEEDIEEFLRDYFDLDVDLEKLYEDWSKKDPRLAKAIDKYRGLRILRQDPFET 116 (117)
T ss_dssp S-HHHHHHCHHHHTTTTS-HHHHHHHHCCHSHHHHHHHHCTTT-------HHHH
T ss_pred cchhhHHHHHHHHhcCCccHHHHHHHHhhhCHHHHHHHhcCCCcEEECCChhhh
Confidence 34567778888999 78888999888666666667776 9999999974
Done!