Query 032215
Match_columns 145
No_of_seqs 53 out of 55
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 11:08:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032215hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00627 UBA: UBA/TS-N domain; 97.3 0.00063 1.4E-08 41.2 4.5 35 95-131 3-37 (37)
2 PF14555 UBA_4: UBA-like domai 97.2 0.00065 1.4E-08 42.5 4.4 39 96-135 2-40 (43)
3 PF02845 CUE: CUE domain; Int 97.1 0.0017 3.7E-08 40.3 5.5 40 96-135 3-42 (42)
4 TIGR00264 alpha-NAC-related pr 96.7 0.0026 5.5E-08 48.9 4.7 39 92-131 76-114 (116)
5 PRK06369 nac nascent polypepti 96.7 0.0028 6.1E-08 48.5 4.7 40 92-132 74-113 (115)
6 cd00194 UBA Ubiquitin Associat 96.4 0.011 2.3E-07 35.2 4.9 35 96-132 3-37 (38)
7 smart00546 CUE Domain that may 96.2 0.013 2.9E-07 36.2 4.6 38 97-134 5-42 (43)
8 smart00165 UBA Ubiquitin assoc 95.7 0.026 5.5E-07 33.5 4.3 35 96-132 3-37 (37)
9 PRK12332 tsf elongation factor 94.3 0.078 1.7E-06 43.4 4.7 41 93-134 3-43 (198)
10 TIGR00116 tsf translation elon 94.2 0.075 1.6E-06 45.9 4.6 41 93-134 3-43 (290)
11 PRK09377 tsf elongation factor 94.1 0.084 1.8E-06 45.6 4.7 40 93-133 4-43 (290)
12 CHL00098 tsf elongation factor 93.8 0.096 2.1E-06 43.0 4.4 38 96-134 3-40 (200)
13 COG1308 EGD2 Transcription fac 93.0 0.22 4.7E-06 38.7 4.8 39 92-131 82-120 (122)
14 COG0264 Tsf Translation elonga 91.5 0.33 7.1E-06 42.5 4.7 40 93-133 4-43 (296)
15 PF06972 DUF1296: Protein of u 86.5 1.8 3.9E-05 30.1 4.6 39 96-134 7-45 (60)
16 PF05861 PhnI: Bacterial phosp 83.8 1.9 4.2E-05 38.8 4.7 42 96-137 43-84 (358)
17 PF03474 DMA: DMRTA motif; In 82.3 1.3 2.7E-05 28.3 2.2 23 110-132 17-39 (39)
18 KOG2239 Transcription factor c 75.4 3.5 7.6E-05 34.7 3.4 38 93-131 170-207 (209)
19 KOG1071 Mitochondrial translat 74.8 5.1 0.00011 35.9 4.5 39 95-134 47-85 (340)
20 PF08938 HBS1_N: HBS1 N-termin 74.4 2.4 5.2E-05 29.5 1.9 40 98-138 35-74 (79)
21 TIGR00601 rad23 UV excision re 72.6 6.6 0.00014 35.1 4.7 37 96-134 158-194 (378)
22 PF00545 Ribonuclease: ribonuc 61.4 3.2 6.9E-05 29.1 0.4 15 39-53 69-83 (83)
23 KOG0011 Nucleotide excision re 61.2 12 0.00026 33.6 4.0 36 96-133 137-172 (340)
24 KOG2606 OTU (ovarian tumor)-li 55.8 3.3 7.1E-05 36.6 -0.4 13 40-52 285-297 (302)
25 PF02954 HTH_8: Bacterial regu 52.0 24 0.00052 21.5 3.2 22 110-131 7-28 (42)
26 PF11626 Rap1_C: TRF2-interact 48.4 32 0.00069 24.2 3.8 33 102-135 4-36 (87)
27 PF12244 DUF3606: Protein of u 48.3 53 0.0012 21.8 4.6 40 91-131 16-55 (57)
28 KOG2561 Adaptor protein NUB1, 45.0 20 0.00043 34.0 2.9 31 105-136 313-343 (568)
29 PF03943 TAP_C: TAP C-terminal 45.0 32 0.0007 22.3 3.1 41 96-137 2-42 (51)
30 COG2103 Predicted sugar phosph 44.7 37 0.00079 30.1 4.3 37 96-133 235-271 (298)
31 PRK05441 murQ N-acetylmuramic 44.1 39 0.00086 28.8 4.3 37 96-133 237-273 (299)
32 KOG1364 Predicted ubiquitin re 43.9 44 0.00095 30.3 4.7 41 96-136 8-48 (356)
33 COG3626 PhnI Uncharacterized e 43.8 37 0.00079 30.5 4.2 42 96-137 43-84 (367)
34 PF10905 DUF2695: Protein of u 40.8 65 0.0014 21.6 4.1 36 101-136 8-44 (53)
35 TIGR00274 N-acetylmuramic acid 38.6 54 0.0012 28.0 4.3 37 96-133 232-268 (291)
36 COG4290 Guanyl-specific ribonu 38.6 9.6 0.00021 30.7 -0.2 15 41-55 138-152 (152)
37 smart00804 TAP_C C-terminal do 32.9 1.6E+02 0.0034 20.1 5.1 39 96-135 14-52 (63)
38 PF03765 CRAL_TRIO_N: CRAL/TRI 31.4 88 0.0019 19.6 3.5 27 105-132 27-53 (55)
39 smart00668 CTLH C-terminal to 30.9 69 0.0015 19.6 2.9 25 109-135 4-28 (58)
40 COG5481 Uncharacterized conser 29.6 52 0.0011 23.2 2.3 25 110-134 9-33 (67)
41 PF01726 LexA_DNA_bind: LexA D 28.7 63 0.0014 21.8 2.6 24 96-119 26-49 (65)
42 cd05007 SIS_Etherase N-acetylm 28.0 41 0.00089 27.9 1.9 32 96-128 224-255 (257)
43 PRK12570 N-acetylmuramic acid- 27.2 1.1E+02 0.0023 26.2 4.3 37 96-133 233-269 (296)
44 PF09957 DUF2191: Uncharacteri 26.7 80 0.0017 20.3 2.7 29 92-120 6-35 (47)
45 KOG0010 Ubiquitin-like protein 25.6 85 0.0018 29.7 3.6 34 100-133 459-492 (493)
46 KOG3450 Huntingtin interacting 25.6 79 0.0017 24.6 2.9 38 95-133 81-118 (119)
47 PHA00617 ribbon-helix-helix do 24.0 76 0.0017 22.9 2.4 25 96-120 52-76 (80)
48 PF12759 HTH_Tnp_IS1: InsA C-t 23.3 53 0.0012 21.6 1.4 20 96-115 13-32 (46)
49 KOG4717 Serine/threonine prote 23.1 1.1E+02 0.0025 30.1 4.1 39 97-135 299-337 (864)
50 PF12651 RHH_3: Ribbon-helix-h 22.7 97 0.0021 19.4 2.5 25 96-120 15-39 (44)
51 COG2904 Uncharacterized protei 22.2 38 0.00083 26.9 0.6 15 16-30 50-64 (137)
52 KOG2934 Uncharacterized conser 20.5 74 0.0016 26.8 2.0 22 102-123 75-96 (204)
No 1
>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=97.27 E-value=0.00063 Score=41.16 Aligned_cols=35 Identities=26% Similarity=0.497 Sum_probs=30.1
Q ss_pred hhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHH
Q 032215 95 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 131 (145)
Q Consensus 95 ~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~L 131 (145)
++.|++++.- |.+ .+.++++|..++||+|.||+||
T Consensus 3 ~~~v~~L~~m-Gf~-~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEM-GFS-REQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHH-TS--HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHc-CCC-HHHHHHHHHHcCCCHHHHHHhC
Confidence 4678888888 866 6699999999999999999997
No 2
>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=97.24 E-value=0.00065 Score=42.54 Aligned_cols=39 Identities=18% Similarity=0.221 Sum_probs=33.2
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHh
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 135 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~ 135 (145)
+.|.++|.-||| +....++.|+.+++|++.||..-++..
T Consensus 2 e~i~~F~~iTg~-~~~~A~~~L~~~~wdle~Av~~y~~~~ 40 (43)
T PF14555_consen 2 EKIAQFMSITGA-DEDVAIQYLEANNWDLEAAVNAYFDDG 40 (43)
T ss_dssp HHHHHHHHHH-S-SHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred HHHHHHHHHHCc-CHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 578999999999 679999999999999999999888754
No 3
>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=97.13 E-value=0.0017 Score=40.27 Aligned_cols=40 Identities=28% Similarity=0.282 Sum_probs=32.9
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHh
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 135 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~ 135 (145)
+.++.+..-+.=-+...|+.+|.+++||+|+||+.|++.+
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~~ 42 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEMS 42 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 4566666666667899999999999999999999999864
No 4
>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=96.75 E-value=0.0026 Score=48.87 Aligned_cols=39 Identities=33% Similarity=0.445 Sum_probs=35.3
Q ss_pred cCchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHH
Q 032215 92 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 131 (145)
Q Consensus 92 ~~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~L 131 (145)
+++++.|+.||..|||+ -+..+++|++++||+-.||.+|
T Consensus 76 ~i~~eDI~lV~eq~gvs-~e~A~~AL~~~~gDl~~AI~~L 114 (116)
T TIGR00264 76 EITEDDIELVMKQCNVS-KEEARRALEECGGDLAEAIMKL 114 (116)
T ss_pred CCCHHHHHHHHHHhCcC-HHHHHHHHHHcCCCHHHHHHHh
Confidence 47778999999999999 5778899999999999999987
No 5
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=96.72 E-value=0.0028 Score=48.46 Aligned_cols=40 Identities=30% Similarity=0.375 Sum_probs=35.8
Q ss_pred cCchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHH
Q 032215 92 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 132 (145)
Q Consensus 92 ~~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Ll 132 (145)
.++++.|+.||..|||+ -+..+++|++++||+-.||.+|-
T Consensus 74 ~i~~edI~lv~~q~gvs-~~~A~~AL~~~~gDl~~AI~~L~ 113 (115)
T PRK06369 74 EIPEEDIELVAEQTGVS-EEEARKALEEANGDLAEAILKLS 113 (115)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHHHHHcCCcHHHHHHHHh
Confidence 46778999999999999 57788999999999999999874
No 6
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=96.39 E-value=0.011 Score=35.24 Aligned_cols=35 Identities=20% Similarity=0.448 Sum_probs=29.3
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 132 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Ll 132 (145)
..+++++. .|.+ .+.++++|+.++||++.|+++|+
T Consensus 3 ~~v~~L~~-mGf~-~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE-MGFS-REEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH-cCCC-HHHHHHHHHHhCCCHHHHHHHHh
Confidence 34556555 5866 99999999999999999999997
No 7
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=96.16 E-value=0.013 Score=36.21 Aligned_cols=38 Identities=21% Similarity=0.221 Sum_probs=30.2
Q ss_pred hHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 97 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 97 ~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
.++.+..-+-=-+...|+.+|++++||+|+||..|+..
T Consensus 5 ~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 5 ALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 45555555444578899999999999999999999864
No 8
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=95.74 E-value=0.026 Score=33.48 Aligned_cols=35 Identities=26% Similarity=0.436 Sum_probs=28.1
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 132 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Ll 132 (145)
..+++++. .| .+.+.++++|..++||++.|+++|+
T Consensus 3 ~~v~~L~~-mG-f~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 3 EKIDQLLE-MG-FSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 34555555 36 6678999999999999999999985
No 9
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=94.30 E-value=0.078 Score=43.38 Aligned_cols=41 Identities=27% Similarity=0.396 Sum_probs=36.2
Q ss_pred CchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 93 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 93 ~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
+.+..|++....||-. +...+++|.+.+||+|.||++|-..
T Consensus 3 i~a~~ik~LR~~tga~-~~~ck~AL~~~~gd~~~A~~~lr~~ 43 (198)
T PRK12332 3 ITAKLVKELREKTGAG-MMDCKKALEEANGDMEKAIEWLREK 43 (198)
T ss_pred CCHHHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 3457899999999976 8899999999999999999999763
No 10
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=94.20 E-value=0.075 Score=45.86 Aligned_cols=41 Identities=24% Similarity=0.316 Sum_probs=36.4
Q ss_pred CchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 93 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 93 ~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
+.+..|++....||.. +.-.+++|.+.+||+|.||++|-..
T Consensus 3 isa~~IK~LRe~Tgag-m~dCKkAL~e~~gDiekAi~~LRkk 43 (290)
T TIGR00116 3 ITAQLVKELRERTGAG-MMDCKKALTEANGDFEKAIKNLRES 43 (290)
T ss_pred CCHHHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 3456899999999998 8889999999999999999999763
No 11
>PRK09377 tsf elongation factor Ts; Provisional
Probab=94.07 E-value=0.084 Score=45.57 Aligned_cols=40 Identities=28% Similarity=0.430 Sum_probs=35.9
Q ss_pred CchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 93 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 93 ~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
+....|++....||.. +.-.+++|++.+||+|.||++|..
T Consensus 4 is~~~IK~LR~~Tgag-m~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 4 ITAALVKELRERTGAG-MMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred cCHHHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3457899999999977 889999999999999999999975
No 12
>CHL00098 tsf elongation factor Ts
Probab=93.85 E-value=0.096 Score=43.02 Aligned_cols=38 Identities=21% Similarity=0.296 Sum_probs=34.6
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
..|++....||.. ..-.+++|.+.+||+|.||++|...
T Consensus 3 ~~ik~LR~~Tgag-~~dck~AL~e~~gd~~~A~~~Lr~~ 40 (200)
T CHL00098 3 ELVKELRDKTGAG-MMDCKKALQEANGDFEKALESLRQK 40 (200)
T ss_pred HHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 5789999999987 8889999999999999999999764
No 13
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=92.95 E-value=0.22 Score=38.74 Aligned_cols=39 Identities=38% Similarity=0.492 Sum_probs=34.0
Q ss_pred cCchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHH
Q 032215 92 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 131 (145)
Q Consensus 92 ~~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~L 131 (145)
.+.++.++.||..||.+ -+-++.+|++.+||+-.||--|
T Consensus 82 ~i~eeDIkLV~eQa~Vs-reeA~kAL~e~~GDlaeAIm~L 120 (122)
T COG1308 82 DISEEDIKLVMEQAGVS-REEAIKALEEAGGDLAEAIMKL 120 (122)
T ss_pred CCCHHHHHHHHHHhCCC-HHHHHHHHHHcCCcHHHHHHHh
Confidence 56678999999999998 5667789999999999999766
No 14
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=91.45 E-value=0.33 Score=42.53 Aligned_cols=40 Identities=28% Similarity=0.422 Sum_probs=35.7
Q ss_pred CchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 93 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 93 ~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
+.+..|++....||-. ....+++|.+.+||+|.||++|-.
T Consensus 4 ita~~VKeLRe~TgAG-MmdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 4 ITAALVKELREKTGAG-MMDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred ccHHHHHHHHHHhCCc-HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3457899999999987 888999999999999999999976
No 15
>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=86.51 E-value=1.8 Score=30.05 Aligned_cols=39 Identities=18% Similarity=0.383 Sum_probs=33.2
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
..||-+-.-+||.+-+-|+.+|.+++.|++.|+.=||.+
T Consensus 7 k~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 7 KTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 346666677899778889999999999999999999875
No 16
>PF05861 PhnI: Bacterial phosphonate metabolism protein (PhnI); InterPro: IPR008773 This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex [].; GO: 0015716 phosphonate transport
Probab=83.76 E-value=1.9 Score=38.77 Aligned_cols=42 Identities=26% Similarity=0.198 Sum_probs=38.9
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHhCC
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 137 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~~~ 137 (145)
-+|.+||..-|-+|.+|..-+|++..||+..||..|-+-|.|
T Consensus 43 lavdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLLRAyRtT 84 (358)
T PF05861_consen 43 LAVDRVMSEGSLYDPELAALAIKQARGDLIEAIFLLRAYRTT 84 (358)
T ss_pred HHHHHHhccccccCHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence 457789999999999999999999999999999999998865
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=82.31 E-value=1.3 Score=28.34 Aligned_cols=23 Identities=35% Similarity=0.466 Sum_probs=18.4
Q ss_pred hHHHHHHHHHhCCChHHHHHHHH
Q 032215 110 SEKVEEVLLQVGGDVDAAIEFLI 132 (145)
Q Consensus 110 ~~LIrq~Le~~~gdvDaAIe~Ll 132 (145)
-.-+..+|..++||+-.|||.++
T Consensus 17 r~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 17 RSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred hHHHHHHHHHcCCcHHHHHHHhC
Confidence 34455689999999999999764
No 18
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=75.37 E-value=3.5 Score=34.70 Aligned_cols=38 Identities=29% Similarity=0.367 Sum_probs=31.6
Q ss_pred CchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHH
Q 032215 93 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 131 (145)
Q Consensus 93 ~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~L 131 (145)
+++..++.||.-.+|+....| ++|.+++||+-.||-.|
T Consensus 170 ve~kDIeLVmsQanvSR~kAV-kALk~~~~DiVnAIM~L 207 (209)
T KOG2239|consen 170 VEAKDIELVMSQANVSRAKAV-KALKNNNNDIVNAIMEL 207 (209)
T ss_pred CchhhHHHHHHHhhhhHHHHH-HHHHhccchHHHHHHHh
Confidence 445679999999999977766 68999999999998654
No 19
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=74.76 E-value=5.1 Score=35.89 Aligned_cols=39 Identities=23% Similarity=0.324 Sum_probs=34.9
Q ss_pred hhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 95 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 95 ~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
..++++....||-+ +..++++|++++||++.|-+||-..
T Consensus 47 ~allk~LR~kTgas-~~ncKkALee~~gDl~~A~~~L~k~ 85 (340)
T KOG1071|consen 47 KALLKKLREKTGAS-MVNCKKALEECGGDLVLAEEWLHKK 85 (340)
T ss_pred HHHHHHHHHHcCCc-HHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 36789999999977 9999999999999999999998644
No 20
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=74.42 E-value=2.4 Score=29.54 Aligned_cols=40 Identities=20% Similarity=0.351 Sum_probs=27.8
Q ss_pred HHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHhCCc
Q 032215 98 IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 138 (145)
Q Consensus 98 V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~~~e 138 (145)
|+.|+.. .+..-.-|+++|-.+.+||+.||.+|+......
T Consensus 35 vr~~Lg~-~~~~e~~i~eal~~~~fDvekAl~~Ll~~~~~~ 74 (79)
T PF08938_consen 35 VREVLGD-YVPPEEQIKEALWHYYFDVEKALDYLLSKFKKK 74 (79)
T ss_dssp HHHHCCC-CC--CCHHHHHHHHTTT-CCHHHHHHHHCCHSS
T ss_pred HHHHHcc-cCCCHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence 4555543 331456678999999999999999999876443
No 21
>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=72.65 E-value=6.6 Score=35.13 Aligned_cols=37 Identities=30% Similarity=0.414 Sum_probs=33.1
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
.+|+.+|.= | ++-+.|+.+|++.=+|.|-|||||+.-
T Consensus 158 ~~I~~i~eM-G-f~R~qV~~ALRAafNNPdRAVEYL~tG 194 (378)
T TIGR00601 158 TTIEEIMEM-G-YEREEVERALRAAFNNPDRAVEYLLTG 194 (378)
T ss_pred HHHHHHHHh-C-CCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence 678999885 5 789999999999999999999999964
No 22
>PF00545 Ribonuclease: ribonuclease; InterPro: IPR000026 Ribonuclease N1 (RNase N1) is a guanine-specific ribonuclease from fungi. RNase T1 and other bacteria RNases are related. The enzyme hydrolyses the phosphodiester bonds in RNA and oligoribonucleotides [], resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.; GO: 0003723 RNA binding, 0004521 endoribonuclease activity; PDB: 1BRK_C 1BAN_C 2F5W_A 1B3S_C 1B2Z_B 1B27_B 3DA7_E 1BSB_C 3Q3F_A 1B20_A ....
Probab=61.41 E-value=3.2 Score=29.12 Aligned_cols=15 Identities=40% Similarity=0.614 Sum_probs=12.8
Q ss_pred HHhcCCCCCCccccC
Q 032215 39 GSYHDGEHYNGVRLK 53 (145)
Q Consensus 39 ISYH~GEHYnSVRri 53 (145)
+-||-|+||+|+.+|
T Consensus 69 ~iy~t~dhy~tF~~~ 83 (83)
T PF00545_consen 69 VIYHTGDHYNTFVRC 83 (83)
T ss_dssp EEEECSSTTSSEEEE
T ss_pred eEEEcCCchhceEeC
Confidence 469999999999864
No 23
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=61.20 E-value=12 Score=33.58 Aligned_cols=36 Identities=25% Similarity=0.424 Sum_probs=32.3
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
.+|+++|.- | ++-+-|+.+|.+-=+|.|.||+||+.
T Consensus 137 ~~V~~Im~M-G-y~re~V~~AlRAafNNPeRAVEYLl~ 172 (340)
T KOG0011|consen 137 QTVQQIMEM-G-YDREEVERALRAAFNNPERAVEYLLN 172 (340)
T ss_pred HHHHHHHHh-C-ccHHHHHHHHHHhhCChhhhHHHHhc
Confidence 678888885 5 89999999999999999999999985
No 24
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=55.78 E-value=3.3 Score=36.56 Aligned_cols=13 Identities=54% Similarity=0.836 Sum_probs=10.2
Q ss_pred HhcCCCCCCcccc
Q 032215 40 SYHDGEHYNGVRL 52 (145)
Q Consensus 40 SYH~GEHYnSVRr 52 (145)
+|--|||||||=.
T Consensus 285 ~y~LGeHYNS~~~ 297 (302)
T KOG2606|consen 285 AYGLGEHYNSVTP 297 (302)
T ss_pred HHHHHhhhccccc
Confidence 4667999999853
No 25
>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=51.98 E-value=24 Score=21.53 Aligned_cols=22 Identities=27% Similarity=0.525 Sum_probs=17.4
Q ss_pred hHHHHHHHHHhCCChHHHHHHH
Q 032215 110 SEKVEEVLLQVGGDVDAAIEFL 131 (145)
Q Consensus 110 ~~LIrq~Le~~~gdvDaAIe~L 131 (145)
-+.|+++|+.++||+..|=..|
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 4678999999999998886655
No 26
>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=48.37 E-value=32 Score=24.17 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=27.0
Q ss_pred HhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHh
Q 032215 102 MAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 135 (145)
Q Consensus 102 m~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~ 135 (145)
|..+|= +...|.++|...+||+..|..|++...
T Consensus 4 ~~~~g~-~~~~v~~aL~~tSgd~~~a~~~vl~~l 36 (87)
T PF11626_consen 4 YEELGY-SREFVTHALYATSGDPELARRFVLNFL 36 (87)
T ss_dssp HHHHTB--HHHHHHHHHHTTTBHHHHHHHHHHCH
T ss_pred HHHhCC-CHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 556665 578888999999999999999888763
No 27
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=48.31 E-value=53 Score=21.76 Aligned_cols=40 Identities=18% Similarity=0.266 Sum_probs=31.8
Q ss_pred CcCchhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHH
Q 032215 91 GIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 131 (145)
Q Consensus 91 d~~~~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~L 131 (145)
+..++-.|+-.+..+||+ .+.++++..+.|.++++.-.||
T Consensus 16 ~~~e~~ev~ywa~~~gvt-~~~L~~AV~~vG~~~~~V~~~L 55 (57)
T PF12244_consen 16 DLSEPYEVRYWAKRFGVT-EEQLREAVRAVGNSRAAVRAYL 55 (57)
T ss_pred CCCCHHHHHHHHHHHCcC-HHHHHHHHHHHCcCHHHHHHHH
Confidence 444557789999999999 6777889999998887766555
No 28
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=45.05 E-value=20 Score=33.98 Aligned_cols=31 Identities=32% Similarity=0.557 Sum_probs=25.1
Q ss_pred CCCCChHHHHHHHHHhCCChHHHHHHHHHHhC
Q 032215 105 SGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 136 (145)
Q Consensus 105 TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~~ 136 (145)
-|=. ....|-+|..++||||+||.|+..+|.
T Consensus 313 mGfe-esdaRlaLRsc~g~Vd~AvqfI~erre 343 (568)
T KOG2561|consen 313 MGFE-ESDARLALRSCNGDVDSAVQFIIERRE 343 (568)
T ss_pred cCCC-chHHHHHHHhccccHHHHHHHHHHHHH
Confidence 3443 556677999999999999999998774
No 29
>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=44.97 E-value=32 Score=22.33 Aligned_cols=41 Identities=12% Similarity=0.095 Sum_probs=32.1
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHhCC
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 137 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~~~ 137 (145)
..|.+++..||=. .+--+..|++++-|.+.|+.........
T Consensus 2 ~mv~~~s~~Tgmn-~~~s~~CL~~n~Wd~~~A~~~F~~l~~~ 42 (51)
T PF03943_consen 2 EMVQQFSQQTGMN-LEWSQKCLEENNWDYERALQNFEELKAQ 42 (51)
T ss_dssp HHHHHHHHHCSS--CCHHHHHHHHTTT-CCHHHHHHHHCCCT
T ss_pred HHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHHHHc
Confidence 3577888888865 6777889999999999999988876654
No 30
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=44.75 E-value=37 Score=30.11 Aligned_cols=37 Identities=35% Similarity=0.745 Sum_probs=32.1
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
.++.-||..|||. -+...+.|++.++++.-||--++.
T Consensus 235 Ra~RIv~~aT~~~-~~~A~~~L~~~~~~vK~AIvm~~~ 271 (298)
T COG2103 235 RAVRIVMEATGCS-AEEAEALLEEAGGNVKLAIVMLLT 271 (298)
T ss_pred HHHHHHHHHhCCC-HHHHHHHHHHcCCccHhHHHHHHh
Confidence 6788999999998 677889999999999999976654
No 31
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=44.09 E-value=39 Score=28.78 Aligned_cols=37 Identities=27% Similarity=0.513 Sum_probs=30.9
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
.++.-||..|||+ .+..+++|++.+|+|--||.-++.
T Consensus 237 ra~~i~~~~~~~~-~~~a~~~l~~~~~~vk~a~~~~~~ 273 (299)
T PRK05441 237 RAVRIVMEATGVS-REEAEAALEAADGSVKLAIVMILT 273 (299)
T ss_pred HHHHHHHHHHCcC-HHHHHHHHHHhCCCcHHHHHHHHh
Confidence 5677899999998 455789999999999999987665
No 32
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=43.86 E-value=44 Score=30.30 Aligned_cols=41 Identities=20% Similarity=0.223 Sum_probs=35.8
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHhC
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 136 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~~ 136 (145)
..|.+||.-|+=..++..+|.|...++|+++||--++...+
T Consensus 8 ~lv~~fl~It~~~t~e~A~q~L~~~~~~le~ai~Lffe~~~ 48 (356)
T KOG1364|consen 8 ALVSKFLAITVQQTVEIATQYLSAADWDLEAAINLFFEHGG 48 (356)
T ss_pred HHHHHHHHHhccccHHHHHHHHHhcCCcHHHHHHHHHHhcc
Confidence 56899999999556999999999999999999988777654
No 33
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=43.80 E-value=37 Score=30.53 Aligned_cols=42 Identities=29% Similarity=0.217 Sum_probs=38.4
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHhCC
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 137 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~~~ 137 (145)
=+|..||..-|-+|-+|.-=++++..||+-.||..|-+-|.+
T Consensus 43 LaVdRVM~EgslyDreLAALAikQa~GD~~EAIFLlRAYRTT 84 (367)
T COG3626 43 LAVDRVMTEGSLYDRELAALALKQASGDLVEAIFLLRAYRTT 84 (367)
T ss_pred hHHHHHhhccchhHHHHHHHHHHHhcchHHHHHHHHHHHHhc
Confidence 468899999999999999999999999999999999988754
No 34
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=40.76 E-value=65 Score=21.61 Aligned_cols=36 Identities=22% Similarity=0.366 Sum_probs=29.4
Q ss_pred HHhcCCCC-ChHHHHHHHHHhCCChHHHHHHHHHHhC
Q 032215 101 VMAGSGCE-NSEKVEEVLLQVGGDVDAAIEFLIAEQG 136 (145)
Q Consensus 101 Vm~~TGC~-D~~LIrq~Le~~~gdvDaAIe~Lla~~~ 136 (145)
-..++||- ++++.++.|....-+.++.+++|-+.-+
T Consensus 8 ~l~~~~CdHtlr~t~~fl~~~~~~~~~vl~~l~~nGg 44 (53)
T PF10905_consen 8 KLSAFGCDHTLRLTRQFLRQRQLDWEDVLEWLRENGG 44 (53)
T ss_pred HcCcCCCCCcHHHHHHHHHHcCCCHHHHHHHHHHcCC
Confidence 34577998 9999999999999999888888765443
No 35
>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=38.64 E-value=54 Score=28.01 Aligned_cols=37 Identities=24% Similarity=0.509 Sum_probs=31.0
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
.++.-|+..|||+ .+-.+++|+..+|+|--||.-++.
T Consensus 232 Ra~~i~~~~~~~~-~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 232 RAVRIVRQATDCN-KELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred HHHHHHHHHhCcC-HHHHHHHHHHhCCCcHHHHHHHHh
Confidence 5677899999998 455889999999999999986654
No 36
>COG4290 Guanyl-specific ribonuclease Sa [Nucleotide transport and metabolism]
Probab=38.63 E-value=9.6 Score=30.65 Aligned_cols=15 Identities=33% Similarity=0.643 Sum_probs=12.3
Q ss_pred hcCCCCCCccccCCC
Q 032215 41 YHDGEHYNGVRLKED 55 (145)
Q Consensus 41 YH~GEHYnSVRri~D 55 (145)
|---+||+|+|||.|
T Consensus 138 YYT~dHY~SFrri~~ 152 (152)
T COG4290 138 YYTSDHYESFRRITD 152 (152)
T ss_pred EEecchhhhhhcccC
Confidence 455689999999975
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=32.86 E-value=1.6e+02 Score=20.07 Aligned_cols=39 Identities=15% Similarity=0.140 Sum_probs=33.4
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHh
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 135 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~ 135 (145)
..|.+++..||=. .+=-+..|++++.|.+.|+....+..
T Consensus 14 ~~v~~~~~~Tgmn-~~~s~~cLe~~~Wd~~~Al~~F~~lk 52 (63)
T smart00804 14 EMVQAFSAQTGMN-AEYSQMCLEDNNWDYERALKNFTELK 52 (63)
T ss_pred HHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 6788888999976 77788899999999999999877744
No 38
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=31.37 E-value=88 Score=19.59 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=20.1
Q ss_pred CCCCChHHHHHHHHHhCCChHHHHHHHH
Q 032215 105 SGCENSEKVEEVLLQVGGDVDAAIEFLI 132 (145)
Q Consensus 105 TGC~D~~LIrq~Le~~~gdvDaAIe~Ll 132 (145)
..|.| ..+...|.+.++||+.|+.-|.
T Consensus 27 ~~~~d-~~llRFLRARkf~v~~A~~mL~ 53 (55)
T PF03765_consen 27 EDHDD-NFLLRFLRARKFDVEKAFKMLK 53 (55)
T ss_dssp SS-SH-HHHHHHHHHTTT-HHHHHHHHH
T ss_pred CCCCH-HHHHHHHHHccCCHHHHHHHHH
Confidence 35566 6666899999999999998764
No 39
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=30.86 E-value=69 Score=19.62 Aligned_cols=25 Identities=32% Similarity=0.627 Sum_probs=18.0
Q ss_pred ChHHHHHHHHHhCCChHHHHHHHHHHh
Q 032215 109 NSEKVEEVLLQVGGDVDAAIEFLIAEQ 135 (145)
Q Consensus 109 D~~LIrq~Le~~~gdvDaAIe~Lla~~ 135 (145)
+...|++.+. .||++.||+++-...
T Consensus 4 ~~~~i~~~i~--~g~~~~a~~~~~~~~ 28 (58)
T smart00668 4 ERKRIRELIL--KGDWDEALEWLSSLK 28 (58)
T ss_pred HHHHHHHHHH--cCCHHHHHHHHHHcC
Confidence 4556767665 789999999885543
No 40
>COG5481 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=29.64 E-value=52 Score=23.23 Aligned_cols=25 Identities=36% Similarity=0.260 Sum_probs=20.6
Q ss_pred hHHHHHHHHHhCCChHHHHHHHHHH
Q 032215 110 SEKVEEVLLQVGGDVDAAIEFLIAE 134 (145)
Q Consensus 110 ~~LIrq~Le~~~gdvDaAIe~Lla~ 134 (145)
.++-..-|.+++-|.|+||-+|++.
T Consensus 9 irl~~arLrqeH~D~DaaInAmi~~ 33 (67)
T COG5481 9 IRLTLARLRQEHADFDAAINAMIAT 33 (67)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHh
Confidence 4555556899999999999999984
No 41
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=28.67 E-value=63 Score=21.82 Aligned_cols=24 Identities=13% Similarity=0.250 Sum_probs=18.9
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQ 119 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~ 119 (145)
.++.+|+.+.|+.+..-|.+-|.+
T Consensus 26 Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 26 PTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp --HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCHHHHHHHhCCCChHHHHHHHHH
Confidence 589999999999999888876654
No 42
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=28.04 E-value=41 Score=27.94 Aligned_cols=32 Identities=41% Similarity=0.692 Sum_probs=26.7
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAI 128 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAI 128 (145)
.++.-||..|||+ -+..+++|+..+|++--||
T Consensus 224 ra~~i~~~~~~~~-~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 224 RAIRIVMEATGVS-RDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHHCcC-HHHHHHHHHHhCCCceeee
Confidence 5677899999998 4457789999999998876
No 43
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=27.21 E-value=1.1e+02 Score=26.23 Aligned_cols=37 Identities=27% Similarity=0.624 Sum_probs=29.6
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
.++.-|+..|||+ .+..+++|+..+|+|--||.-++.
T Consensus 233 Ra~~i~~~~~~~~-~~~a~~~l~~~~~~vk~ai~~~~~ 269 (296)
T PRK12570 233 RAVRIVMQATGCS-EDEAKELLKESDNDVKLAILMILT 269 (296)
T ss_pred HHHHHHHHHHCcC-HHHHHHHHHHhCCccHHHHHHHHh
Confidence 5677788899998 445778999999999999876554
No 44
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=26.67 E-value=80 Score=20.26 Aligned_cols=29 Identities=24% Similarity=0.282 Sum_probs=21.2
Q ss_pred cCchhhHHHHHhcCCCC-ChHHHHHHHHHh
Q 032215 92 IINAGSIKLVMAGSGCE-NSEKVEEVLLQV 120 (145)
Q Consensus 92 ~~~~~~V~~Vm~~TGC~-D~~LIrq~Le~~ 120 (145)
.+|++.++++|.-||.. -.+.|.++|++.
T Consensus 6 ~iDd~Ll~eA~~l~g~~tk~~~V~~ALr~~ 35 (47)
T PF09957_consen 6 DIDDELLAEAMRLTGTKTKKEAVNEALREL 35 (47)
T ss_pred eeCHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence 34557889999999976 556777777654
No 45
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=25.58 E-value=85 Score=29.66 Aligned_cols=34 Identities=29% Similarity=0.416 Sum_probs=29.3
Q ss_pred HHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 100 LVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 100 ~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
+-.+.-|-.|.+.-.|+|.+-+|||.+|||-|+.
T Consensus 459 eQL~~MGF~nre~nlqAL~atgGdi~aAverll~ 492 (493)
T KOG0010|consen 459 EQLNDMGFLDREANLQALRATGGDINAAVERLLG 492 (493)
T ss_pred HHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence 3445668889999999999999999999999874
No 46
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=25.58 E-value=79 Score=24.59 Aligned_cols=38 Identities=24% Similarity=0.267 Sum_probs=28.1
Q ss_pred hhhHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHH
Q 032215 95 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 133 (145)
Q Consensus 95 ~~~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla 133 (145)
...++.|||.--.+ -.-++..|.+..||+-+|..+|+.
T Consensus 81 keDlelImnELei~-k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 81 KEDLELIMNELEIS-KAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHhcccHHHHHHHHhc
Confidence 35678888853332 344677899999999999998874
No 47
>PHA00617 ribbon-helix-helix domain containing protein
Probab=23.99 E-value=76 Score=22.90 Aligned_cols=25 Identities=20% Similarity=0.162 Sum_probs=21.6
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHh
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQV 120 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~ 120 (145)
..+...+..+|++...+|+++|.+.
T Consensus 52 erLD~LA~~~GrsRSelIreAI~~Y 76 (80)
T PHA00617 52 AKLEQVAIKMKKSKSEIIREALEKY 76 (80)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 4577888899999999999999875
No 48
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=23.29 E-value=53 Score=21.64 Aligned_cols=20 Identities=20% Similarity=0.478 Sum_probs=16.5
Q ss_pred hhHHHHHhcCCCCChHHHHH
Q 032215 96 GSIKLVMAGSGCENSEKVEE 115 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq 115 (145)
.-|+-+|++.||.|...|-.
T Consensus 13 qIvema~nG~GiRdtaRvL~ 32 (46)
T PF12759_consen 13 QIVEMAFNGSGIRDTARVLK 32 (46)
T ss_pred HHHHHHhcCCcchhhHhHhc
Confidence 56788999999999987744
No 49
>KOG4717 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=23.15 E-value=1.1e+02 Score=30.10 Aligned_cols=39 Identities=23% Similarity=0.201 Sum_probs=32.4
Q ss_pred hHHHHHhcCCCCChHHHHHHHHHhCCChHHHHHHHHHHh
Q 032215 97 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 135 (145)
Q Consensus 97 ~V~~Vm~~TGC~D~~LIrq~Le~~~gdvDaAIe~Lla~~ 135 (145)
.+-+-|..-...+-+-|.++|+.+.||--.|-.|||||+
T Consensus 299 ~IIq~Mv~G~IAs~e~Il~aLe~n~YNhiTATYfLLAEr 337 (864)
T KOG4717|consen 299 TIIQQMVAGAIASEEDILRALENNEYNHITATYFLLAER 337 (864)
T ss_pred HHHHHHhcccccCHHHHHHHHhccccchhhhHHHHHHHH
Confidence 343444444777899999999999999999999999997
No 50
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=22.65 E-value=97 Score=19.40 Aligned_cols=25 Identities=20% Similarity=0.237 Sum_probs=20.3
Q ss_pred hhHHHHHhcCCCCChHHHHHHHHHh
Q 032215 96 GSIKLVMAGSGCENSEKVEEVLLQV 120 (145)
Q Consensus 96 ~~V~~Vm~~TGC~D~~LIrq~Le~~ 120 (145)
.....+...||++-..+|+++|++.
T Consensus 15 ~~L~~ls~~t~i~~S~Ll~eAle~~ 39 (44)
T PF12651_consen 15 EKLKELSEETGIPKSKLLREALEDY 39 (44)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3467788899999999999988764
No 51
>COG2904 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.16 E-value=38 Score=26.92 Aligned_cols=15 Identities=47% Similarity=0.793 Sum_probs=11.4
Q ss_pred ccCCCcchhhHHHHH
Q 032215 16 EHGPDIWNCKQLLLL 30 (145)
Q Consensus 16 ~~~~~~~~~~~~~~~ 30 (145)
-||-|||+|-.|-.|
T Consensus 50 f~G~DiW~~YElSwL 64 (137)
T COG2904 50 FHGADIWTLYELSWL 64 (137)
T ss_pred ccccchhhhhhhhhh
Confidence 489999998766544
No 52
>KOG2934 consensus Uncharacterized conserved protein, contains Josephin domain [General function prediction only]
Probab=20.47 E-value=74 Score=26.77 Aligned_cols=22 Identities=23% Similarity=0.294 Sum_probs=19.7
Q ss_pred HhcCCCCChHHHHHHHHHhCCC
Q 032215 102 MAGSGCENSEKVEEVLLQVGGD 123 (145)
Q Consensus 102 m~~TGC~D~~LIrq~Le~~~gd 123 (145)
|.++||+|++-|-.+|...+.-
T Consensus 75 ~~g~Gnydvnvimaalq~~gl~ 96 (204)
T KOG2934|consen 75 WKGPGNYDVNVIMAALQQCGLE 96 (204)
T ss_pred ccCCCcccHHHHHHHHHhcCce
Confidence 6789999999999999998865
Done!