Query 002640
Match_columns 897
No_of_seqs 124 out of 145
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:07:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002640.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002640hhsearch_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 4.9E-25 1.1E-29 185.1 3.9 59 20-78 1-60 (60)
2 PF02845 CUE: CUE domain; Int 97.8 2.7E-05 5.8E-10 61.6 4.1 38 25-62 2-40 (42)
3 smart00546 CUE Domain that may 97.1 0.00072 1.6E-08 53.7 4.5 40 24-63 2-42 (43)
4 PF00627 UBA: UBA/TS-N domain; 97.1 0.00068 1.5E-08 52.4 4.2 35 25-60 3-37 (37)
5 cd00194 UBA Ubiquitin Associat 96.8 0.0017 3.8E-08 49.7 4.4 37 25-62 2-38 (38)
6 smart00165 UBA Ubiquitin assoc 96.8 0.0018 4E-08 49.4 4.2 36 25-61 2-37 (37)
7 PF14555 UBA_4: UBA-like domai 94.9 0.032 7E-07 44.6 3.7 38 25-62 1-38 (43)
8 PRK06369 nac nascent polypepti 93.7 0.08 1.7E-06 51.4 4.3 39 24-62 76-114 (115)
9 TIGR00264 alpha-NAC-related pr 93.5 0.086 1.9E-06 51.3 4.2 39 24-62 78-116 (116)
10 COG1308 EGD2 Transcription fac 92.6 0.14 3E-06 50.2 4.1 39 24-62 84-122 (122)
11 PRK09377 tsf elongation factor 92.4 0.12 2.5E-06 57.0 3.7 38 25-62 6-43 (290)
12 CHL00098 tsf elongation factor 91.8 0.13 2.9E-06 53.9 3.2 37 26-62 3-39 (200)
13 PF11547 E3_UbLigase_EDD: E3 u 91.8 0.24 5.3E-06 41.8 4.0 38 25-62 10-48 (53)
14 TIGR00601 rad23 UV excision re 91.4 0.19 4.1E-06 57.1 4.1 41 22-63 154-194 (378)
15 TIGR00116 tsf translation elon 91.1 0.19 4.1E-06 55.5 3.5 37 26-62 6-42 (290)
16 PRK12332 tsf elongation factor 90.5 0.21 4.6E-06 52.3 3.2 37 26-62 6-42 (198)
17 PF03474 DMA: DMRTA motif; In 89.2 0.41 8.9E-06 38.7 3.1 36 26-61 3-39 (39)
18 PF08938 HBS1_N: HBS1 N-termin 88.9 0.15 3.2E-06 45.9 0.5 37 26-62 30-69 (79)
19 COG0264 Tsf Translation elonga 87.9 0.53 1.2E-05 52.1 4.0 37 26-62 7-43 (296)
20 KOG1071 Mitochondrial translat 83.8 0.85 1.9E-05 51.1 3.1 42 22-63 44-85 (340)
21 KOG0943 Predicted ubiquitin-pr 78.3 3.3 7.1E-05 53.0 5.6 48 16-63 179-229 (3015)
22 KOG0011 Nucleotide excision re 75.6 3 6.5E-05 47.1 4.0 41 22-63 133-173 (340)
23 TIGR00601 rad23 UV excision re 58.2 17 0.00036 41.9 5.5 45 18-63 331-375 (378)
24 TIGR00274 N-acetylmuramic acid 53.0 13 0.00027 41.2 3.4 48 24-71 230-277 (291)
25 KOG0011 Nucleotide excision re 51.7 23 0.0005 40.3 5.2 49 17-67 291-339 (340)
26 PRK05441 murQ N-acetylmuramic 51.0 14 0.00031 40.8 3.4 47 25-71 236-282 (299)
27 PF08006 DUF1700: Protein of u 43.0 18 0.0004 36.7 2.6 40 20-63 17-63 (181)
28 PF08828 DSX_dimer: Doublesex 41.0 22 0.00047 31.7 2.3 38 26-63 8-48 (62)
29 KOG0418 Ubiquitin-protein liga 40.5 39 0.00084 36.0 4.4 44 18-62 156-199 (200)
30 PRK12570 N-acetylmuramic acid- 37.0 37 0.00079 37.7 3.9 40 24-63 231-270 (296)
31 PF03943 TAP_C: TAP C-terminal 35.2 28 0.00061 29.4 2.1 38 25-62 1-38 (51)
32 KOG0010 Ubiquitin-like protein 32.5 51 0.0011 39.4 4.3 48 15-62 445-492 (493)
33 PF11626 Rap1_C: TRF2-interact 32.1 43 0.00094 30.7 2.9 31 33-63 5-35 (87)
34 PHA02616 VP2/VP3; Provisional 29.9 35 0.00076 36.6 2.2 29 39-69 185-217 (259)
35 COG2103 Predicted sugar phosph 29.1 52 0.0011 36.9 3.3 55 17-71 222-280 (298)
36 smart00804 TAP_C C-terminal do 27.1 1E+02 0.0023 27.3 4.3 43 19-61 7-49 (63)
37 PF05918 API5: Apoptosis inhib 25.1 24 0.00052 42.7 0.0 7 65-71 460-466 (556)
38 PF02954 HTH_8: Bacterial regu 24.7 67 0.0015 25.6 2.5 21 40-60 8-28 (42)
39 KOG3816 Cell differentiation r 20.8 1.9E+02 0.0041 34.2 5.8 18 413-432 386-403 (526)
40 KOG2561 Adaptor protein NUB1, 20.2 93 0.002 37.2 3.4 27 36-62 314-340 (568)
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=99.90 E-value=4.9e-25 Score=185.06 Aligned_cols=59 Identities=86% Similarity=1.268 Sum_probs=57.4
Q ss_pred CCcchHHHHHhhhhccCC-ChHHHHHHHhhcCCCHHHHHHHhhcCCCccccccccccccc
Q 002640 20 IPAGSRKIVQSLKEIVNC-PESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKSKRDKRKE 78 (897)
Q Consensus 20 ip~~~rk~V~~ikEi~~~-seedi~~aL~ecn~D~n~Av~rLl~~~~~~EVkkKr~kkKe 78 (897)
||+++||+||.||||+++ ||+|||+||+|||||||||++|||+||+|||||+||+||||
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=97.78 E-value=2.7e-05 Score=61.65 Aligned_cols=38 Identities=32% Similarity=0.433 Sum_probs=35.6
Q ss_pred HHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 25 RKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 25 rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
+.+|++||||| +|+++.|..+|++|++|++.||+.||+
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=97.11 E-value=0.00072 Score=53.69 Aligned_cols=40 Identities=28% Similarity=0.388 Sum_probs=37.3
Q ss_pred hHHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 24 SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 24 ~rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
..+.|..|+|+| +.+++.|-..|++|++|++.||+.||+.
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 457899999999 9999999999999999999999999984
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=97.10 E-value=0.00068 Score=52.38 Aligned_cols=35 Identities=29% Similarity=0.421 Sum_probs=32.1
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHh
Q 002640 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRL 60 (897)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rL 60 (897)
+++|++|+|+ |.+++++..||+.|++|+++||+.|
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=96.84 E-value=0.0017 Score=49.69 Aligned_cols=37 Identities=24% Similarity=0.312 Sum_probs=34.2
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
+++|++|+++ |.+++++..||+-|++|++.|++.|++
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 5789999997 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=96.80 E-value=0.0018 Score=49.40 Aligned_cols=36 Identities=22% Similarity=0.305 Sum_probs=33.6
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhh
Q 002640 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (897)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl 61 (897)
+++|++|+++ |.+++++..||+.|++|++.|++.|+
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 6789999999 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=94.91 E-value=0.032 Score=44.64 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=33.4
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
+++|.+.++|+|++++.....|+.||.|++.||+..++
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=93.72 E-value=0.08 Score=51.41 Aligned_cols=39 Identities=28% Similarity=0.285 Sum_probs=35.7
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
..+.|..|+|-+++|+++...||++||+|+-+||-.|-+
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 467889999999999999999999999999999988754
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=93.54 E-value=0.086 Score=51.27 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=35.1
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
..+.|..|+|-+++|+++...||++||||+-+||-+|.+
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 357788899999999999999999999999999988753
No 10
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=92.63 E-value=0.14 Score=50.21 Aligned_cols=39 Identities=23% Similarity=0.240 Sum_probs=34.8
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
.++-|+.+.|=++.|++|...||++||||+-+||-+|.+
T Consensus 84 ~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~~ 122 (122)
T COG1308 84 SEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLTE 122 (122)
T ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhcC
Confidence 356788888889999999999999999999999999863
No 11
>PRK09377 tsf elongation factor Ts; Provisional
Probab=92.37 E-value=0.12 Score=57.04 Aligned_cols=38 Identities=21% Similarity=0.238 Sum_probs=35.1
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
-+.|+.|||.||..--||..||.+||+|.+.|++.|-+
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 46799999999999999999999999999999998755
No 12
>CHL00098 tsf elongation factor Ts
Probab=91.81 E-value=0.13 Score=53.87 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=34.4
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
+.|+.|||.||..--||..||.+|++|.+.|++.|-+
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 5799999999999999999999999999999997754
No 13
>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=91.77 E-value=0.24 Score=41.78 Aligned_cols=38 Identities=29% Similarity=0.397 Sum_probs=31.4
Q ss_pred HHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 25 RKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 25 rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
++.|.+...+. |++.+-|+.-|+-+|.|+|+||+-||+
T Consensus 10 edlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLs 48 (53)
T PF11547_consen 10 EDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLS 48 (53)
T ss_dssp HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhc
Confidence 45566666677 999999999999999999999999997
No 14
>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=91.38 E-value=0.19 Score=57.14 Aligned_cols=41 Identities=20% Similarity=0.350 Sum_probs=38.7
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
...+.+|+.|+|| ||.+++|..||+-+.++|++||+.||.|
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 3678999999999 9999999999999999999999999996
No 15
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=91.07 E-value=0.19 Score=55.46 Aligned_cols=37 Identities=24% Similarity=0.287 Sum_probs=34.5
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
+.|+.|||.||..--||..||.||++|.+.||+.|=+
T Consensus 6 ~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRk 42 (290)
T TIGR00116 6 QLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRE 42 (290)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5799999999999999999999999999999997755
No 16
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=90.55 E-value=0.21 Score=52.28 Aligned_cols=37 Identities=27% Similarity=0.311 Sum_probs=34.5
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
+.|+.|||.||..--||-.||.+|++|.+.|++.|-+
T Consensus 6 ~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~ 42 (198)
T PRK12332 6 KLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLRE 42 (198)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6799999999999999999999999999999997755
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=89.17 E-value=0.41 Score=38.74 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=31.5
Q ss_pred HHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhh
Q 002640 26 KIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLL 61 (897)
Q Consensus 26 k~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl 61 (897)
.-+..|..+| ......+=.+|+-|+||+-.||+.+|
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 3467788899 88899999999999999999999765
No 18
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=88.94 E-value=0.15 Score=45.95 Aligned_cols=37 Identities=27% Similarity=0.425 Sum_probs=30.4
Q ss_pred HHHHhhhhcc--CC-ChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 26 KIVQSLKEIV--NC-PESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 26 k~V~~ikEi~--~~-seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
.-+..||+++ .. ++.+|.-||-.|++|++.||..||+
T Consensus 30 ~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 30 SCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp HHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 4456788888 35 8999999999999999999999987
No 19
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=87.85 E-value=0.53 Score=52.14 Aligned_cols=37 Identities=24% Similarity=0.277 Sum_probs=34.1
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
+.|+.|||.||..=-||..||.||+||.+.||+.|=+
T Consensus 7 ~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 7 ALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred HHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5789999999999999999999999999999997644
No 20
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=83.80 E-value=0.85 Score=51.07 Aligned_cols=42 Identities=24% Similarity=0.277 Sum_probs=38.8
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
++....|++|||-||.+-.+|.++|.|||+|+..|...|-+.
T Consensus 44 ~~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~ 85 (340)
T KOG1071|consen 44 ASSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKK 85 (340)
T ss_pred cccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 367899999999999999999999999999999999988764
No 21
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=78.32 E-value=3.3 Score=53.01 Aligned_cols=48 Identities=31% Similarity=0.522 Sum_probs=41.8
Q ss_pred CcccCCcc--hHHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 16 GISSIPAG--SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 16 ~~~~ip~~--~rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
++-.||+. .++.|.+..-|+ |++.+-|+.-|+.++.|+|+||+-||+.
T Consensus 179 gaPriPAsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLSR 229 (3015)
T KOG0943|consen 179 GAPRIPASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLSR 229 (3015)
T ss_pred CCCcCCcccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhcc
Confidence 45567754 588999988888 9999999999999999999999999965
No 22
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=75.60 E-value=3 Score=47.08 Aligned_cols=41 Identities=24% Similarity=0.341 Sum_probs=37.9
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
...+.+|++|+|| ||..|++.+||+-.-..|++||+.||.+
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 3567889999999 9999999999999999999999999995
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=58.21 E-value=17 Score=41.91 Aligned_cols=45 Identities=18% Similarity=0.280 Sum_probs=41.5
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 18 ~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
..|-..-|+.|+.|+++ ||.+..++-|.--|+-+.+.|++.|+++
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 56667889999999999 9999999999999999999999999984
No 24
>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=52.98 E-value=13 Score=41.18 Aligned_cols=48 Identities=17% Similarity=0.206 Sum_probs=39.4
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcccccc
Q 002640 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (897)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~~~~~EVkk 71 (897)
+++-+..|++++|+++++...+|++|++++-.||--++.+-.+.|-++
T Consensus 230 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~~~~~~~a~~ 277 (291)
T TIGR00274 230 KARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMILSTLSASEAKV 277 (291)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 445567788999999999999999999999999998877555555544
No 25
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=51.66 E-value=23 Score=40.31 Aligned_cols=49 Identities=18% Similarity=0.376 Sum_probs=41.1
Q ss_pred cccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcc
Q 002640 17 ISSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFH 67 (897)
Q Consensus 17 ~~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~~~~~ 67 (897)
.+.+-..-++-|..||.+ |..+.=++-|.--|+=+.+.|++.||++. |.
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 344556778889999988 88888899999999999999999999954 54
No 26
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=50.96 E-value=14 Score=40.82 Aligned_cols=47 Identities=19% Similarity=0.153 Sum_probs=38.2
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcccccc
Q 002640 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (897)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~~~~~EVkk 71 (897)
++-+..|++++|+++++...+|++|++++-.||-.++.+-.+.+-++
T Consensus 236 ~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~~~~~~a~~ 282 (299)
T PRK05441 236 DRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMILTGLDAAEAKA 282 (299)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 34456788899999999999999999999999998887545555444
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=42.97 E-value=18 Score=36.66 Aligned_cols=40 Identities=28% Similarity=0.439 Sum_probs=32.2
Q ss_pred CC-cchHHHHHhhhhcc------CCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 20 IP-AGSRKIVQSLKEIV------NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 20 ip-~~~rk~V~~ikEi~------~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
+| .+.++.++-.+|.| |.|||||++.| |||.+.+..|+..
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 55 35777788888877 47899999887 8999999988874
No 28
>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=40.98 E-value=22 Score=31.71 Aligned_cols=38 Identities=29% Similarity=0.331 Sum_probs=27.7
Q ss_pred HHHHhhhhccCCChH---HHHHHHhhcCCCHHHHHHHhhcC
Q 002640 26 KIVQSLKEIVNCPES---EIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 26 k~V~~ikEi~~~see---di~~aL~ecn~D~n~Av~rLl~~ 63 (897)
+--+.|.|-|+.+=| =.|++|++.+.|++||..||-|+
T Consensus 8 ~~cqkLlEkf~YpWEmmpLmyVILK~A~~D~eeA~rrI~E~ 48 (62)
T PF08828_consen 8 ERCQKLLEKFRYPWEMMPLMYVILKYADADVEEASRRIDEA 48 (62)
T ss_dssp HHHHHHHHHTT--GGGHHHHHHHHHHTTT-HHHHHHHHHH-
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 445678888855433 46889999999999999999985
No 29
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.48 E-value=39 Score=36.03 Aligned_cols=44 Identities=27% Similarity=0.265 Sum_probs=39.2
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 18 ~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
...-....++|..|+|+ |.++++++.+|.--+-+.++|.+-||+
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 34456788999999999 999999999999999999999998887
No 30
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=36.99 E-value=37 Score=37.72 Aligned_cols=40 Identities=25% Similarity=0.372 Sum_probs=34.3
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
+++-+..|++++|+++++.-.+|++|++++-.||-.++.+
T Consensus 231 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~~ 270 (296)
T PRK12570 231 VARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMILTG 270 (296)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHhC
Confidence 4455677889999999999999999999999999877664
No 31
>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=35.16 E-value=28 Score=29.38 Aligned_cols=38 Identities=18% Similarity=0.156 Sum_probs=30.4
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
.++|..+.+.+|.+.+=...-|+|++-|.+.|+....+
T Consensus 1 q~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 1 QEMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 36788999999888888888999999999999985443
No 32
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=32.50 E-value=51 Score=39.37 Aligned_cols=48 Identities=19% Similarity=0.162 Sum_probs=42.3
Q ss_pred CCcccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 15 NGISSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 15 ~~~~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
...+.++..+...+++|.++.=...|+-+.||.-+++|++.||+|||.
T Consensus 445 ~~~~~pe~r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~ 492 (493)
T KOG0010|consen 445 QQTVPPEERYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLG 492 (493)
T ss_pred cCCCCchHHHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence 356777788889999999997667899999999999999999999985
No 33
>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=32.12 E-value=43 Score=30.71 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=25.9
Q ss_pred hccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002640 33 EIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (897)
Q Consensus 33 Ei~~~seedi~~aL~ecn~D~n~Av~rLl~~ 63 (897)
+-+|.+++.|..||.-|.||+..|...||..
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 3449999999999999999999999977754
No 34
>PHA02616 VP2/VP3; Provisional
Probab=29.93 E-value=35 Score=36.64 Aligned_cols=29 Identities=41% Similarity=0.434 Sum_probs=21.7
Q ss_pred hHHHHHHHhhcCCCHHH----HHHHhhcCCCcccc
Q 002640 39 ESEIYAMLKECNMDPNE----AVNRLLSQDPFHEV 69 (897)
Q Consensus 39 eedi~~aL~ecn~D~n~----Av~rLl~~~~~~EV 69 (897)
.+=|+++|+|.|-|.++ ||.|- ||-.|-|
T Consensus 185 PdWiLyVLEeLn~di~kiptq~vkrk--q~~lh~~ 217 (259)
T PHA02616 185 PDWILYVLEELNKDIYKIPTQAVKRK--QDELHPV 217 (259)
T ss_pred hHHHHHHHHHHHHHHhhcchhhhhhh--ccccCcC
Confidence 35589999999988877 55543 6777777
No 35
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=29.10 E-value=52 Score=36.94 Aligned_cols=55 Identities=25% Similarity=0.323 Sum_probs=42.5
Q ss_pred cccCCcchHHH----HHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcccccc
Q 002640 17 ISSIPAGSRKI----VQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (897)
Q Consensus 17 ~~~ip~~~rk~----V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~~~~~~EVkk 71 (897)
-+.+-++-+|. +..|+|++|++.||--++|++|++++-.||--++.+-.-+|-++
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 35566666665 45678888999999999999999999999988877544444444
No 36
>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=27.09 E-value=1e+02 Score=27.30 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=36.9
Q ss_pred cCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhh
Q 002640 19 SIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (897)
Q Consensus 19 ~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl 61 (897)
.+...-+.+|..+.+.++.+-+=....|+++|-|.+.|+....
T Consensus 7 ~~~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~ 49 (63)
T smart00804 7 TLSPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFT 49 (63)
T ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3445668899999999999999999999999999999998443
No 37
>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=25.08 E-value=24 Score=42.69 Aligned_cols=7 Identities=29% Similarity=0.553 Sum_probs=2.3
Q ss_pred Ccccccc
Q 002640 65 PFHEVKS 71 (897)
Q Consensus 65 ~~~EVkk 71 (897)
+|-+.+|
T Consensus 460 SWk~~~~ 466 (556)
T PF05918_consen 460 SWKEAKK 466 (556)
T ss_dssp TTS----
T ss_pred eeeeccc
Confidence 5888866
No 38
>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=24.70 E-value=67 Score=25.60 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=17.1
Q ss_pred HHHHHHHhhcCCCHHHHHHHh
Q 002640 40 SEIYAMLKECNMDPNEAVNRL 60 (897)
Q Consensus 40 edi~~aL~ecn~D~n~Av~rL 60 (897)
+-|..+|+.|+++..+|...|
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 39
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=20.75 E-value=1.9e+02 Score=34.19 Aligned_cols=18 Identities=33% Similarity=0.366 Sum_probs=9.4
Q ss_pred eCCCccccCCCCCccccccc
Q 002640 413 IPNHLQVHSSDCSHLSFGSF 432 (897)
Q Consensus 413 IPnHLQV~~adc~~LSFGSF 432 (897)
-=+-|.|. |+.-|-=|+|
T Consensus 386 C~~~L~Vf--dkyPLVDG~f 403 (526)
T KOG3816|consen 386 CKDELKVF--DKYPLVDGVF 403 (526)
T ss_pred hccchhhh--cccccccceE
Confidence 33444443 4556666666
No 40
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=20.24 E-value=93 Score=37.20 Aligned_cols=27 Identities=30% Similarity=0.448 Sum_probs=24.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002640 36 NCPESEIYAMLKECNMDPNEAVNRLLS 62 (897)
Q Consensus 36 ~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (897)
|.-+-|---||+-|++|++.||+.|.+
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~e 340 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIE 340 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHH
Confidence 566777888999999999999999998
Done!