Query 002894
Match_columns 869
No_of_seqs 119 out of 136
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 12:56:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002894.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002894hhsearch_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 9.2E-26 2E-30 188.7 4.0 59 20-78 1-60 (60)
2 PF02845 CUE: CUE domain; Int 97.8 2.6E-05 5.6E-10 61.6 4.1 38 25-62 2-40 (42)
3 PF00627 UBA: UBA/TS-N domain; 97.2 0.00047 1E-08 53.1 4.2 35 25-60 3-37 (37)
4 smart00546 CUE Domain that may 97.1 0.00069 1.5E-08 53.7 4.5 39 24-62 2-41 (43)
5 cd00194 UBA Ubiquitin Associat 96.9 0.0013 2.7E-08 50.4 4.4 37 25-62 2-38 (38)
6 smart00165 UBA Ubiquitin assoc 96.9 0.0013 2.9E-08 50.0 4.2 36 25-61 2-37 (37)
7 PF14555 UBA_4: UBA-like domai 95.2 0.025 5.3E-07 45.2 3.9 38 25-62 1-38 (43)
8 PRK06369 nac nascent polypepti 93.9 0.069 1.5E-06 51.7 4.3 39 24-62 76-114 (115)
9 TIGR00264 alpha-NAC-related pr 93.8 0.072 1.6E-06 51.6 4.1 39 24-62 78-116 (116)
10 COG1308 EGD2 Transcription fac 92.8 0.13 2.7E-06 50.3 4.1 38 25-62 85-122 (122)
11 PRK09377 tsf elongation factor 92.8 0.095 2.1E-06 57.6 3.7 38 25-62 6-43 (290)
12 PF11547 E3_UbLigase_EDD: E3 u 92.4 0.18 3.9E-06 42.3 4.0 39 25-63 10-49 (53)
13 CHL00098 tsf elongation factor 92.3 0.11 2.4E-06 54.4 3.3 37 26-62 3-39 (200)
14 TIGR00116 tsf translation elon 91.6 0.16 3.4E-06 56.0 3.6 37 26-62 6-42 (290)
15 TIGR00601 rad23 UV excision re 91.5 0.18 3.9E-06 57.3 4.1 41 22-63 154-194 (378)
16 PRK12332 tsf elongation factor 91.2 0.17 3.8E-06 52.8 3.3 37 26-62 6-42 (198)
17 PF08938 HBS1_N: HBS1 N-termin 90.7 0.089 1.9E-06 47.2 0.6 37 26-62 30-69 (79)
18 PF03474 DMA: DMRTA motif; In 89.0 0.43 9.4E-06 38.4 3.1 36 26-61 3-39 (39)
19 COG0264 Tsf Translation elonga 87.0 0.59 1.3E-05 51.7 3.7 38 25-62 6-43 (296)
20 KOG1071 Mitochondrial translat 86.0 0.51 1.1E-05 52.6 2.6 42 22-63 44-85 (340)
21 KOG0943 Predicted ubiquitin-pr 82.4 2 4.3E-05 54.7 5.6 48 16-63 179-229 (3015)
22 KOG0011 Nucleotide excision re 75.3 3.1 6.6E-05 46.9 4.0 41 22-63 133-173 (340)
23 TIGR00601 rad23 UV excision re 63.7 12 0.00025 43.1 5.5 45 18-63 331-375 (378)
24 KOG0011 Nucleotide excision re 58.0 16 0.00034 41.5 5.1 49 17-67 291-339 (340)
25 TIGR00274 N-acetylmuramic acid 56.0 11 0.00023 41.6 3.5 48 24-71 230-277 (291)
26 PRK05441 murQ N-acetylmuramic 54.0 12 0.00026 41.3 3.5 47 25-71 236-282 (299)
27 PHA02616 VP2/VP3; Provisional 46.8 11 0.00025 40.0 1.7 38 39-78 185-228 (259)
28 PF08006 DUF1700: Protein of u 45.1 17 0.00036 36.9 2.6 40 20-63 17-63 (181)
29 PRK12570 N-acetylmuramic acid- 40.1 31 0.00066 38.3 3.9 40 24-63 231-270 (296)
30 KOG0418 Ubiquitin-protein liga 39.3 41 0.0009 35.7 4.4 44 18-62 156-199 (200)
31 PF08828 DSX_dimer: Doublesex 38.5 25 0.00054 31.2 2.3 39 25-63 7-48 (62)
32 PF11626 Rap1_C: TRF2-interact 36.6 33 0.00071 31.4 2.9 31 33-63 5-35 (87)
33 KOG0010 Ubiquitin-like protein 34.9 50 0.0011 39.3 4.7 47 16-62 446-492 (493)
34 COG5222 Uncharacterized conser 33.8 40 0.00087 38.0 3.5 35 636-678 378-412 (427)
35 KOG3816 Cell differentiation r 32.5 82 0.0018 36.8 5.7 10 423-432 394-403 (526)
36 COG2103 Predicted sugar phosph 32.4 43 0.00093 37.4 3.4 55 17-71 222-280 (298)
37 smart00804 TAP_C C-terminal do 30.1 87 0.0019 27.7 4.3 43 19-61 7-49 (63)
38 PF03943 TAP_C: TAP C-terminal 28.7 51 0.0011 27.7 2.6 38 25-62 1-38 (51)
39 KOG2561 Adaptor protein NUB1, 28.5 35 0.00076 40.4 2.1 27 36-62 314-340 (568)
40 PF02954 HTH_8: Bacterial regu 26.8 58 0.0013 25.8 2.5 21 40-60 8-28 (42)
41 PF05918 API5: Apoptosis inhib 23.3 27 0.00059 42.2 0.0 7 65-71 460-466 (556)
42 KOG3248 Transcription factor T 22.6 35 0.00075 39.1 0.6 29 42-71 207-235 (421)
43 PF11705 RNA_pol_3_Rpc31: DNA- 20.1 67 0.0015 34.2 2.1 10 1-10 1-10 (233)
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=9.2e-26 Score=188.69 Aligned_cols=59 Identities=86% Similarity=1.268 Sum_probs=57.4
Q ss_pred CCcchHHHHHhhhhccCC-ChHHHHHHHhhcCCCHHHHHHHhhcCCCccccccccccccc
Q 002894 20 IPAGSRKIVQSLKEIVNC-PESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKSKRDKRKE 78 (869)
Q Consensus 20 ip~~~rk~V~~ikEi~~~-seedi~~aL~ecn~D~n~Av~rLl~q~~~~EVkkKr~kkKe 78 (869)
||+++||+||.||||+++ ||+|||+||+|||||||||++|||+||+|||||+||+||||
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=97.79 E-value=2.6e-05 Score=61.59 Aligned_cols=38 Identities=32% Similarity=0.433 Sum_probs=35.5
Q ss_pred HHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 25 RKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 25 rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
+.+|++||||| +|+++.|..+|++|++|++.||+.||+
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
>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=97.20 E-value=0.00047 Score=53.11 Aligned_cols=35 Identities=29% Similarity=0.421 Sum_probs=32.2
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHh
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRL 60 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rL 60 (869)
+++|++|+++ |.+++++..||+.|++|+++||+.|
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 9999999999999999999999866
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=97.12 E-value=0.00069 Score=53.66 Aligned_cols=39 Identities=28% Similarity=0.406 Sum_probs=36.9
Q ss_pred hHHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 24 SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 24 ~rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
..+.|..|+|+| +.+++.|..+|++|++|++.||+.||+
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 457899999999 999999999999999999999999997
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=96.94 E-value=0.0013 Score=50.35 Aligned_cols=37 Identities=24% Similarity=0.312 Sum_probs=34.3
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
+++|++|+++ |.+++++..||+-|++|++.|++.|++
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=96.90 E-value=0.0013 Score=50.04 Aligned_cols=36 Identities=22% Similarity=0.305 Sum_probs=33.7
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhh
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl 61 (869)
+++|++|+++ |.+++++..||+.|++|++.|++.|+
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=95.23 E-value=0.025 Score=45.16 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=33.5
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
+++|.+.++|+|++++.....|+.||.|++.||+..++
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 57899999999999999999999999999999997665
No 8
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=93.92 E-value=0.069 Score=51.66 Aligned_cols=39 Identities=28% Similarity=0.285 Sum_probs=35.6
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
..+.|+.|+|-+|+|+++...||++||+|+-+||-.|-+
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 467889999999999999999999999999999987754
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=93.81 E-value=0.072 Score=51.63 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=35.0
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
..+.|..|+|-+|+|+++...||++||+|+-+||-+|-+
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=92.81 E-value=0.13 Score=50.32 Aligned_cols=38 Identities=21% Similarity=0.227 Sum_probs=34.4
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
++-|+-+.|=++.|++|...||+|||||+-+||-+|.+
T Consensus 85 eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~~ 122 (122)
T COG1308 85 EEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLTE 122 (122)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhcC
Confidence 56788888888999999999999999999999999863
No 11
>PRK09377 tsf elongation factor Ts; Provisional
Probab=92.80 E-value=0.095 Score=57.62 Aligned_cols=38 Identities=21% Similarity=0.238 Sum_probs=35.2
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
-+.|+.|||.||..--||..||.|||+|.+.|++.|-+
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
>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=92.42 E-value=0.18 Score=42.26 Aligned_cols=39 Identities=28% Similarity=0.399 Sum_probs=31.8
Q ss_pred HHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 25 RKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 25 rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
++.|.+...++ |++.+-|+.-|+-+|.|+|+||+-||+.
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 45566666677 9999999999999999999999999973
No 13
>CHL00098 tsf elongation factor Ts
Probab=92.33 E-value=0.11 Score=54.44 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=34.5
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
+.|+.|||.||..--||..||.+|++|.+.|++.|-+
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 14
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=91.60 E-value=0.16 Score=55.98 Aligned_cols=37 Identities=24% Similarity=0.287 Sum_probs=34.5
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
+.|+.|||.||..--||..||.||++|.+.|++.|-+
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 15
>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=91.54 E-value=0.18 Score=57.27 Aligned_cols=41 Identities=20% Similarity=0.350 Sum_probs=38.6
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
...+.+|+.|+|| ||.+++|..||+-+.++|++||+.||.+
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 3668999999999 9999999999999999999999999995
No 16
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=91.18 E-value=0.17 Score=52.83 Aligned_cols=37 Identities=27% Similarity=0.311 Sum_probs=34.6
Q ss_pred HHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 26 KIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 26 k~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
+.|+.|||.||..--||..||.+|++|.+.|+..|-+
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 17
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=90.72 E-value=0.089 Score=47.18 Aligned_cols=37 Identities=27% Similarity=0.425 Sum_probs=30.4
Q ss_pred HHHHhhhhcc--CC-ChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 26 KIVQSLKEIV--NC-PESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 26 k~V~~ikEi~--~~-seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
.-+.+||+++ .. ++.+|.-||-.|++|++.||..||+
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 8999999999999999999999998
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=88.96 E-value=0.43 Score=38.41 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=31.4
Q ss_pred HHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhh
Q 002894 26 KIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLL 61 (869)
Q Consensus 26 k~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl 61 (869)
.-+..|..+| ......+=.+|+-|+||+-.||+.+|
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 88899999999999999999999765
No 19
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=87.00 E-value=0.59 Score=51.66 Aligned_cols=38 Identities=24% Similarity=0.265 Sum_probs=34.6
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
-+.|+.|||.||..=-||..||.||+||.+.||+.|=+
T Consensus 6 a~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 6 AALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 36799999999999999999999999999999997754
No 20
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=86.00 E-value=0.51 Score=52.64 Aligned_cols=42 Identities=24% Similarity=0.277 Sum_probs=38.8
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
++....|++|||-||.+-.+|.++|.|||+|...|...|-+.
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=82.36 E-value=2 Score=54.66 Aligned_cols=48 Identities=31% Similarity=0.522 Sum_probs=41.5
Q ss_pred CcccCCcc--hHHHHHhhhhcc-CCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 16 GISSIPAG--SRKIVQSLKEIV-NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 16 ~~~~ip~~--~rk~V~~ikEi~-~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
++-.||+. .++.|.+..-|+ |++.+-|+.-|+.+|.|+|+||+-||+.
T Consensus 179 gaPriPAsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLSR 229 (3015)
T KOG0943|consen 179 GAPRIPASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLSR 229 (3015)
T ss_pred CCCcCCcccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhcc
Confidence 44556654 488899988888 9999999999999999999999999976
No 22
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=75.34 E-value=3.1 Score=46.88 Aligned_cols=41 Identities=24% Similarity=0.341 Sum_probs=37.9
Q ss_pred cchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 22 AGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 22 ~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
...+.+|++|.|| ||-.|++..||+-.-..|+.||+.||.+
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 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=63.75 E-value=12 Score=43.08 Aligned_cols=45 Identities=18% Similarity=0.280 Sum_probs=41.4
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 18 ~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
..|-..-|+.|+.|+++ ||.+..++-|..-|+-+.+.|++.||++
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 56667888999999999 9999999999999999999999999984
No 24
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=58.01 E-value=16 Score=41.46 Aligned_cols=49 Identities=18% Similarity=0.376 Sum_probs=41.1
Q ss_pred cccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcc
Q 002894 17 ISSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFH 67 (869)
Q Consensus 17 ~~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q~~~~ 67 (869)
.+.+-..-++-|..||.+ |..+.=++-|.--|+=+.+.|++.||++. |+
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 89888899999999999999999999954 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=55.95 E-value=11 Score=41.65 Aligned_cols=48 Identities=17% Similarity=0.206 Sum_probs=39.4
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcccccc
Q 002894 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (869)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q~~~~EVkk 71 (869)
+++-+..|++++|++++|...+|.+|++++-.||--++..-.+.|-++
T Consensus 230 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~~~~~~~a~~ 277 (291)
T TIGR00274 230 KARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMILSTLSASEAKV 277 (291)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 455567788999999999999999999999999998877545555544
No 26
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=53.95 E-value=12 Score=41.30 Aligned_cols=47 Identities=19% Similarity=0.153 Sum_probs=38.2
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcccccc
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q~~~~EVkk 71 (869)
++-+..|.+++|+++++...+|++|++++-.||-.++..-.+.+-++
T Consensus 236 ~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~~~~~~a~~ 282 (299)
T PRK05441 236 DRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMILTGLDAAEAKA 282 (299)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhCCCHHHHHH
Confidence 34456788899999999999999999999999998887545555544
No 27
>PHA02616 VP2/VP3; Provisional
Probab=46.76 E-value=11 Score=39.97 Aligned_cols=38 Identities=37% Similarity=0.372 Sum_probs=25.6
Q ss_pred hHHHHHHHhhcCCCHHH----HHHHhhcCCCcccc--ccccccccc
Q 002894 39 ESEIYAMLKECNMDPNE----AVNRLLSQDPFHEV--KSKRDKRKE 78 (869)
Q Consensus 39 eedi~~aL~ecn~D~n~----Av~rLl~q~~~~EV--kkKr~kkKe 78 (869)
.+=|+++|+|.|-|.++ ||.|- ||-.|-| .||+.+.|+
T Consensus 185 PdWiLyVLEeLn~di~kiptq~vkrk--q~~lh~~~~~kk~~~skK 228 (259)
T PHA02616 185 PDWILYVLEELNKDIYKIPTQAVKRK--QDELHPVSPTKKAALSKK 228 (259)
T ss_pred hHHHHHHHHHHHHHHhhcchhhhhhh--ccccCcCCchhhHHHHhh
Confidence 35589999999998887 55553 6778888 334433333
No 28
>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=45.05 E-value=17 Score=36.94 Aligned_cols=40 Identities=28% Similarity=0.439 Sum_probs=31.7
Q ss_pred CC-cchHHHHHhhhhcc------CCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 20 IP-AGSRKIVQSLKEIV------NCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 20 ip-~~~rk~V~~ikEi~------~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
+| .+.++.++-.+|.| |.|||||++-| |||.+.+..++..
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 45 34677778888877 57899999887 8999999988873
No 29
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=40.07 E-value=31 Score=38.26 Aligned_cols=40 Identities=25% Similarity=0.372 Sum_probs=34.2
Q ss_pred hHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 24 SRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 24 ~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
+++-+..|++++|+++++.-.+|++|++++-.||-.++..
T Consensus 231 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~~ 270 (296)
T PRK12570 231 VARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMILTG 270 (296)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHhC
Confidence 4455677889999999999999999999999999877663
No 30
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.28 E-value=41 Score=35.67 Aligned_cols=44 Identities=27% Similarity=0.265 Sum_probs=39.2
Q ss_pred ccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 18 SSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 18 ~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
...-....++|..|+|+ |.++++++.+|.--+-+.++|.+-||+
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 34446788999999999 999999999999999999999998886
No 31
>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=38.48 E-value=25 Score=31.17 Aligned_cols=39 Identities=28% Similarity=0.304 Sum_probs=28.2
Q ss_pred HHHHHhhhhccCCChH---HHHHHHhhcCCCHHHHHHHhhcC
Q 002894 25 RKIVQSLKEIVNCPES---EIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 25 rk~V~~ikEi~~~see---di~~aL~ecn~D~n~Av~rLl~q 63 (869)
-+--+.|.|-|+.+=| =.|++|++.+.|++||..||-+.
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 3445778888865533 46899999999999999999884
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=36.59 E-value=33 Score=31.40 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=26.0
Q ss_pred hccCCChHHHHHHHhhcCCCHHHHHHHhhcC
Q 002894 33 EIVNCPESEIYAMLKECNMDPNEAVNRLLSQ 63 (869)
Q Consensus 33 Ei~~~seedi~~aL~ecn~D~n~Av~rLl~q 63 (869)
+-+|.+++.|..||.-|.||+..|...||..
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 33
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=34.86 E-value=50 Score=39.35 Aligned_cols=47 Identities=19% Similarity=0.160 Sum_probs=41.8
Q ss_pred CcccCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 16 GISSIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 16 ~~~~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
..+.++..+..-+++|.++.=...|+-+.||.-+++|++.||+|||.
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 46777788889999999997667899999999999999999999985
No 34
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.78 E-value=40 Score=38.03 Aligned_cols=35 Identities=23% Similarity=0.369 Sum_probs=20.8
Q ss_pred CCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCC
Q 002894 636 MPGASVATGPALPPHLAVHPYSQPTLPLGHFANMIGYPFLPQS 678 (869)
Q Consensus 636 ~ps~~i~~~~~~pQ~l~~hpY~Qp~~pl~hy~N~~~Ypylp~~ 678 (869)
.|..--++++|+|.++ ||+- +++|| |||-|+|||-
T Consensus 378 ~pa~~~~~~~p~p~~p--~~~g-----~ppfp-m~plp~mpp~ 412 (427)
T COG5222 378 EPAFKSAMAIPMPSMP--HVQG-----FPPFP-MMPLPQMPPM 412 (427)
T ss_pred cchhhhcCCCCCCCCC--ccCC-----CCCCC-CCCCCCCCcc
Confidence 4444456677888775 4443 22466 8887765554
No 35
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=32.50 E-value=82 Score=36.84 Aligned_cols=10 Identities=40% Similarity=0.335 Sum_probs=5.7
Q ss_pred CCCccccccc
Q 002894 423 DCSHLSFGSF 432 (869)
Q Consensus 423 ec~hLSFGSF 432 (869)
|+.-|==|+|
T Consensus 394 dkyPLVDG~f 403 (526)
T KOG3816|consen 394 DKYPLVDGVF 403 (526)
T ss_pred cccccccceE
Confidence 4555555666
No 36
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=32.43 E-value=43 Score=37.40 Aligned_cols=55 Identities=25% Similarity=0.323 Sum_probs=42.1
Q ss_pred cccCCcchHHH----HHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhcCCCcccccc
Q 002894 17 ISSIPAGSRKI----VQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (869)
Q Consensus 17 ~~~ip~~~rk~----V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~q~~~~EVkk 71 (869)
-+.+-++-+|. +..|+|++|++.||--++|++|++++-.||--++..-.-+|-++
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 45678888999999999999999999999988777544444444
No 37
>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=30.15 E-value=87 Score=27.65 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=37.1
Q ss_pred cCCcchHHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhh
Q 002894 19 SIPAGSRKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLL 61 (869)
Q Consensus 19 ~ip~~~rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl 61 (869)
.+...-+.+|..+.+.++.+-+=....|+++|-|.+.|+....
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 38
>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=28.70 E-value=51 Score=27.73 Aligned_cols=38 Identities=18% Similarity=0.156 Sum_probs=30.7
Q ss_pred HHHHHhhhhccCCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 25 RKIVQSLKEIVNCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 25 rk~V~~ikEi~~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
.++|..+...+|.+.+=...-|+||+-|.+.|+....+
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 36889999999888888889999999999999985443
No 39
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=28.50 E-value=35 Score=40.39 Aligned_cols=27 Identities=30% Similarity=0.448 Sum_probs=24.3
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHhhc
Q 002894 36 NCPESEIYAMLKECNMDPNEAVNRLLS 62 (869)
Q Consensus 36 ~~seedi~~aL~ecn~D~n~Av~rLl~ 62 (869)
|.-+-|---||+-|++|++.||++|.+
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~e 340 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIE 340 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHH
Confidence 566777888999999999999999998
No 40
>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=26.75 E-value=58 Score=25.85 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=17.1
Q ss_pred HHHHHHHhhcCCCHHHHHHHh
Q 002894 40 SEIYAMLKECNMDPNEAVNRL 60 (869)
Q Consensus 40 edi~~aL~ecn~D~n~Av~rL 60 (869)
+-|..+|+.|+++..+|...|
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 457889999999999998855
No 41
>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=23.29 E-value=27 Score=42.16 Aligned_cols=7 Identities=29% Similarity=0.553 Sum_probs=2.3
Q ss_pred Ccccccc
Q 002894 65 PFHEVKS 71 (869)
Q Consensus 65 ~~~EVkk 71 (869)
+|-+.+|
T Consensus 460 SWk~~~~ 466 (556)
T PF05918_consen 460 SWKEAKK 466 (556)
T ss_dssp TTS----
T ss_pred eeeeccc
Confidence 5888866
No 42
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=22.59 E-value=35 Score=39.05 Aligned_cols=29 Identities=21% Similarity=0.523 Sum_probs=22.5
Q ss_pred HHHHHhhcCCCHHHHHHHhhcCCCcccccc
Q 002894 42 IYAMLKECNMDPNEAVNRLLSQDPFHEVKS 71 (869)
Q Consensus 42 i~~aL~ecn~D~n~Av~rLl~q~~~~EVkk 71 (869)
--++|.||..-...||+.||- --||.+.|
T Consensus 207 Ra~vvaEctlKeSAaiNqiLG-rRWH~LSr 235 (421)
T KOG3248|consen 207 RAKVVAECTLKESAAINQILG-RRWHALSR 235 (421)
T ss_pred HHHHHHHhhhhhHHHHHHHHh-HHHhhhhH
Confidence 346788999999999999996 56766654
No 43
>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=20.08 E-value=67 Score=34.22 Aligned_cols=10 Identities=70% Similarity=1.262 Sum_probs=4.9
Q ss_pred CCCCCCCCCC
Q 002894 1 MSGKGGGGGV 10 (869)
Q Consensus 1 m~~~~~g~~~ 10 (869)
|||-|||||+
T Consensus 1 MSgRGggrg~ 10 (233)
T PF11705_consen 1 MSGRGGGRGG 10 (233)
T ss_pred CCCCCCCCCC
Confidence 8853333333
Done!