Query 032619
Match_columns 137
No_of_seqs 102 out of 112
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 03:46:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032619.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032619hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02845 CUE: CUE domain; Int 97.7 0.00018 3.9E-09 43.7 5.6 40 88-127 3-42 (42)
2 PF00627 UBA: UBA/TS-N domain; 97.6 0.00011 2.3E-09 43.5 4.4 35 87-123 3-37 (37)
3 PF14555 UBA_4: UBA-like domai 97.4 0.00029 6.2E-09 43.1 4.4 40 88-128 2-41 (43)
4 KOG2606 OTU (ovarian tumor)-li 97.4 7E-05 1.5E-09 63.3 1.7 44 1-45 250-298 (302)
5 TIGR00264 alpha-NAC-related pr 97.3 0.00044 9.4E-09 51.5 4.8 40 84-124 76-115 (116)
6 PRK06369 nac nascent polypepti 97.2 0.00058 1.2E-08 50.7 4.8 40 84-124 74-113 (115)
7 cd00194 UBA Ubiquitin Associat 97.1 0.0018 3.9E-08 37.9 5.0 34 89-124 4-37 (38)
8 smart00546 CUE Domain that may 97.1 0.0015 3.2E-08 39.6 4.7 39 88-126 4-42 (43)
9 smart00165 UBA Ubiquitin assoc 96.5 0.0072 1.6E-07 35.1 4.4 34 89-124 4-37 (37)
10 COG1308 EGD2 Transcription fac 95.8 0.021 4.5E-07 42.9 5.0 41 83-124 81-121 (122)
11 TIGR00116 tsf translation elon 93.7 0.12 2.7E-06 43.6 4.9 41 85-126 3-43 (290)
12 PF06972 DUF1296: Protein of u 93.7 0.17 3.7E-06 33.7 4.6 39 89-127 8-46 (60)
13 PRK12332 tsf elongation factor 93.7 0.14 3.1E-06 40.9 5.0 41 85-126 3-43 (198)
14 PRK09377 tsf elongation factor 93.5 0.14 3.1E-06 43.2 5.0 41 85-126 4-44 (290)
15 CHL00098 tsf elongation factor 92.8 0.21 4.5E-06 40.2 4.7 38 88-126 3-40 (200)
16 PF03474 DMA: DMRTA motif; In 92.4 0.16 3.4E-06 31.2 2.8 25 100-124 15-39 (39)
17 COG0264 Tsf Translation elonga 90.1 0.61 1.3E-05 39.8 5.0 40 85-125 4-43 (296)
18 PF08938 HBS1_N: HBS1 N-termin 84.1 0.75 1.6E-05 31.4 1.9 40 89-129 34-73 (79)
19 TIGR00601 rad23 UV excision re 83.4 2.2 4.7E-05 37.4 4.8 38 87-126 157-194 (378)
20 PF02954 HTH_8: Bacterial regu 82.8 2 4.3E-05 25.7 3.2 22 102-123 7-28 (42)
21 PF05861 PhnI: Bacterial phosp 80.0 3.5 7.5E-05 36.1 4.8 43 88-130 43-85 (358)
22 KOG1071 Mitochondrial translat 79.7 3.3 7.2E-05 35.9 4.6 45 85-130 45-89 (340)
23 COG2103 Predicted sugar phosph 76.0 4.6 9.9E-05 34.5 4.3 38 87-125 234-271 (298)
24 KOG2239 Transcription factor c 72.7 5.8 0.00013 32.3 4.0 36 87-123 172-207 (209)
25 PF11626 Rap1_C: TRF2-interact 70.4 7.4 0.00016 26.8 3.7 33 94-127 4-36 (87)
26 PRK05441 murQ N-acetylmuramic 69.3 8.1 0.00017 32.4 4.3 38 87-125 236-273 (299)
27 TIGR00274 N-acetylmuramic acid 65.0 11 0.00024 31.5 4.3 38 87-125 231-268 (291)
28 KOG0011 Nucleotide excision re 62.9 13 0.00028 32.4 4.4 38 87-126 136-173 (340)
29 KOG2561 Adaptor protein NUB1, 61.4 5.9 0.00013 36.2 2.1 99 27-130 239-345 (568)
30 KOG0010 Ubiquitin-like protein 61.3 10 0.00023 34.5 3.7 33 93-125 460-492 (493)
31 PF03943 TAP_C: TAP C-terminal 57.5 12 0.00026 23.6 2.5 42 89-131 3-44 (51)
32 PF09957 DUF2191: Uncharacteri 56.0 15 0.00033 22.8 2.8 28 85-112 7-35 (47)
33 PRK12570 N-acetylmuramic acid- 55.5 20 0.00044 30.0 4.3 38 87-125 232-269 (296)
34 PF11547 E3_UbLigase_EDD: E3 u 53.8 58 0.0013 21.0 5.3 43 86-128 9-51 (53)
35 smart00804 TAP_C C-terminal do 53.0 53 0.0011 21.7 5.2 42 87-129 13-54 (63)
36 PF00545 Ribonuclease: ribonuc 49.7 8.7 0.00019 26.3 1.0 16 29-44 67-82 (83)
37 KOG3450 Huntingtin interacting 49.2 23 0.00051 26.4 3.2 41 84-125 78-118 (119)
38 cd05007 SIS_Etherase N-acetylm 46.2 13 0.00029 30.3 1.8 33 87-120 223-255 (257)
39 PF12244 DUF3606: Protein of u 46.1 58 0.0013 20.9 4.5 37 86-123 19-55 (57)
40 KOG1364 Predicted ubiquitin re 45.9 38 0.00083 29.7 4.6 40 88-127 8-47 (356)
41 PF10905 DUF2695: Protein of u 44.2 71 0.0015 20.6 4.6 35 91-125 6-41 (53)
42 KOG4167 Predicted DNA-binding 41.6 31 0.00067 33.4 3.6 30 98-127 573-602 (907)
43 smart00668 CTLH C-terminal to 41.5 38 0.00082 20.4 3.0 25 101-127 4-28 (58)
44 COG3626 PhnI Uncharacterized e 40.8 47 0.001 28.8 4.3 42 89-130 44-85 (367)
45 KOG2934 Uncharacterized conser 40.0 22 0.00048 28.7 2.0 22 94-115 75-96 (204)
46 PF03765 CRAL_TRIO_N: CRAL/TRI 39.7 58 0.0012 19.9 3.6 28 96-124 26-53 (55)
47 COG4290 Guanyl-specific ribonu 33.6 15 0.00033 28.4 0.2 15 33-47 138-152 (152)
48 PRK01905 DNA-binding protein F 32.6 67 0.0015 21.4 3.3 23 101-123 38-60 (77)
49 KOG4077 Cytochrome c oxidase, 32.5 1E+02 0.0023 23.8 4.6 45 83-127 61-111 (149)
50 PF02338 OTU: OTU-like cystein 31.9 47 0.001 23.0 2.5 35 1-35 72-112 (121)
51 cd00923 Cyt_c_Oxidase_Va Cytoc 31.5 1E+02 0.0022 22.6 4.2 43 85-127 21-69 (103)
52 PRK05441 murQ N-acetylmuramic 30.0 82 0.0018 26.4 4.0 33 89-122 265-297 (299)
53 TIGR00601 rad23 UV excision re 28.1 1.2E+02 0.0026 26.7 4.8 38 88-127 339-376 (378)
54 PRK00430 fis global DNA-bindin 27.9 84 0.0018 22.1 3.2 23 101-123 56-78 (95)
55 PF02284 COX5A: Cytochrome c o 26.8 1.5E+02 0.0032 21.9 4.4 45 84-128 23-73 (108)
56 PF12651 RHH_3: Ribbon-helix-h 26.5 78 0.0017 19.2 2.5 25 88-112 15-39 (44)
57 KOG2605 OTU (ovarian tumor)-li 25.4 35 0.00077 30.0 1.1 116 6-128 138-256 (371)
58 PRK12570 N-acetylmuramic acid- 24.8 1.1E+02 0.0023 25.7 3.9 32 89-121 261-292 (296)
59 PHA00617 ribbon-helix-helix do 24.5 1.7E+02 0.0037 20.3 4.2 25 88-112 52-76 (80)
60 TIGR00274 N-acetylmuramic acid 24.4 93 0.002 26.0 3.4 32 89-121 260-291 (291)
61 PF12759 HTH_Tnp_IS1: InsA C-t 23.7 66 0.0014 20.3 1.8 21 87-107 12-32 (46)
62 PRK10923 glnG nitrogen regulat 21.0 1.1E+02 0.0024 26.3 3.3 22 102-123 431-452 (469)
63 PF01726 LexA_DNA_bind: LexA D 21.0 1E+02 0.0022 20.1 2.4 23 89-111 27-49 (65)
64 TIGR02974 phageshock_pspF psp 20.5 1.1E+02 0.0024 25.8 3.1 22 102-123 294-315 (329)
No 1
>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=97.66 E-value=0.00018 Score=43.69 Aligned_cols=40 Identities=28% Similarity=0.282 Sum_probs=34.7
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 127 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~ 127 (137)
+.++.+..-.+=.+.+.|+.+|++++||+|.||+.||+++
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 4677778888888999999999999999999999999864
No 2
>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=97.65 E-value=0.00011 Score=43.53 Aligned_cols=35 Identities=26% Similarity=0.497 Sum_probs=30.1
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~L 123 (137)
++.+++++.- |+. .+.++++|+.++||+|.|+++|
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 5678888888 755 7799999999999999999987
No 3
>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=97.44 E-value=0.00029 Score=43.10 Aligned_cols=40 Identities=18% Similarity=0.209 Sum_probs=33.2
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhc
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 128 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~ 128 (137)
+.|...|.-||| +.+..++.|+.+++|++.||..-++...
T Consensus 2 e~i~~F~~iTg~-~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 2 EKIAQFMSITGA-DEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHH-S-SHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred HHHHHHHHHHCc-CHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 578999999999 6799999999999999999998877543
No 4
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=97.40 E-value=7e-05 Score=63.33 Aligned_cols=44 Identities=25% Similarity=0.357 Sum_probs=33.2
Q ss_pred CcceeEEEEeCCCcceEEeeccCCCceEEEEE-----ecCCCcccccccC
Q 032619 1 MYCLLLSLMQHMSPRWYIRNFDYHEARMIHLS-----YHDGEHYNGVRLK 45 (137)
Q Consensus 1 ~~~~~i~Ihq~~~p~w~I~~~~~~~~~~lhla-----Yh~geHYnSVR~~ 45 (137)
+|+++|.|+|.+.|+-.+.- +.+.-+.|-|. |.+|||||||-..
T Consensus 250 vL~~PI~Vy~~~~p~~~~ge-ey~kd~pL~lvY~rH~y~LGeHYNS~~~~ 298 (302)
T KOG2606|consen 250 VLQVPIEVYQADGPILEYGE-EYGKDKPLILVYHRHAYGLGEHYNSVTPL 298 (302)
T ss_pred hhccCeEEeecCCCceeech-hhCCCCCeeeehHHhHHHHHhhhcccccc
Confidence 48999999999999777663 33233667787 5579999998653
No 5
>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=97.31 E-value=0.00044 Score=51.49 Aligned_cols=40 Identities=33% Similarity=0.411 Sum_probs=36.1
Q ss_pred CCChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 032619 84 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 124 (137)
Q Consensus 84 ~~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll 124 (137)
.++++.|+.||..|||+ .+..+++|++|+||+-.||.+|-
T Consensus 76 ~i~~eDI~lV~eq~gvs-~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 76 EITEDDIELVMKQCNVS-KEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred CCCHHHHHHHHHHhCcC-HHHHHHHHHHcCCCHHHHHHHhh
Confidence 36678899999999998 78899999999999999999873
No 6
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=97.24 E-value=0.00058 Score=50.75 Aligned_cols=40 Identities=30% Similarity=0.375 Sum_probs=36.5
Q ss_pred CCChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 032619 84 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 124 (137)
Q Consensus 84 ~~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll 124 (137)
.++++.|+.||..|||+ .+..+++|++++||+-.||.+|-
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 46688899999999998 78899999999999999999885
No 7
>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=97.09 E-value=0.0018 Score=37.89 Aligned_cols=34 Identities=21% Similarity=0.469 Sum_probs=28.3
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 124 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll 124 (137)
.++.++. .|.. .+.++++|..++||++.|+++|+
T Consensus 4 ~v~~L~~-mGf~-~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 4 KLEQLLE-MGFS-REEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-cCCC-HHHHHHHHHHhCCCHHHHHHHHh
Confidence 4555444 6765 99999999999999999999987
No 8
>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=97.07 E-value=0.0015 Score=39.64 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=33.8
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 126 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~ 126 (137)
..++.++.-..=-+...|+.+|+.++||+|.||+.||.+
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 356677777777889999999999999999999999965
No 9
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=96.48 E-value=0.0072 Score=35.14 Aligned_cols=34 Identities=26% Similarity=0.457 Sum_probs=27.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 124 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll 124 (137)
.+++++. .| .+.+.++++|..++||++.|+++|+
T Consensus 4 ~v~~L~~-mG-f~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 4 KIDQLLE-MG-FSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 3444443 45 6688999999999999999999985
No 10
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=95.80 E-value=0.021 Score=42.91 Aligned_cols=41 Identities=37% Similarity=0.466 Sum_probs=36.5
Q ss_pred CCCChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 032619 83 GIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 124 (137)
Q Consensus 83 ~~~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll 124 (137)
..++++.|+.||..||.+ .+.++.+|++++||+-.||..|.
T Consensus 81 ~~i~eeDIkLV~eQa~Vs-reeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 81 SDISEEDIKLVMEQAGVS-REEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred CCCCHHHHHHHHHHhCCC-HHHHHHHHHHcCCcHHHHHHHhc
Confidence 346688999999999998 88888999999999999998874
No 11
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=93.70 E-value=0.12 Score=43.63 Aligned_cols=41 Identities=24% Similarity=0.316 Sum_probs=36.3
Q ss_pred CChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q 032619 85 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 126 (137)
Q Consensus 85 ~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~ 126 (137)
++...|++.-..||.. ..-.+++|.+++||+|.||++|...
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 3456799999999998 8889999999999999999999864
No 12
>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=93.69 E-value=0.17 Score=33.70 Aligned_cols=39 Identities=18% Similarity=0.400 Sum_probs=32.9
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 127 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~ 127 (137)
.|+-+-.-+||..-+-|..+|.+|+.|.+.|+..||..+
T Consensus 8 ~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~qD 46 (60)
T PF06972_consen 8 TVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQD 46 (60)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Confidence 466666688996677899999999999999999999743
No 13
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=93.66 E-value=0.14 Score=40.94 Aligned_cols=41 Identities=27% Similarity=0.396 Sum_probs=36.1
Q ss_pred CChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q 032619 85 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 126 (137)
Q Consensus 85 ~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~ 126 (137)
++...|++.-..||.. ....+++|.+++||+|.||++|..-
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 3456899999999976 8889999999999999999999863
No 14
>PRK09377 tsf elongation factor Ts; Provisional
Probab=93.50 E-value=0.14 Score=43.24 Aligned_cols=41 Identities=27% Similarity=0.429 Sum_probs=36.1
Q ss_pred CChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q 032619 85 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 126 (137)
Q Consensus 85 ~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~ 126 (137)
++...|++.-..||.. ..-.+++|++++||+|.||++|...
T Consensus 4 is~~~IK~LR~~Tgag-m~dCKkAL~e~~gD~ekAi~~Lrk~ 44 (290)
T PRK09377 4 ITAALVKELRERTGAG-MMDCKKALTEADGDIEKAIEWLRKK 44 (290)
T ss_pred cCHHHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 3456899999999977 8889999999999999999999863
No 15
>CHL00098 tsf elongation factor Ts
Probab=92.78 E-value=0.21 Score=40.20 Aligned_cols=38 Identities=21% Similarity=0.296 Sum_probs=33.8
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 126 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~ 126 (137)
..|++.-..||.. ..-.+++|..++||+|.||++|..-
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 4688888899976 8889999999999999999999864
No 16
>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=92.44 E-value=0.16 Score=31.16 Aligned_cols=25 Identities=32% Similarity=0.462 Sum_probs=21.1
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHHH
Q 032619 100 ENSEKVEEVLLQVGGDVDAAIEFLI 124 (137)
Q Consensus 100 ~D~~lIre~L~~~~gdvdaAI~~Ll 124 (137)
.....+.-+|+.|+||+-.|||.++
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHhC
Confidence 4566777899999999999999874
No 17
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=90.13 E-value=0.61 Score=39.80 Aligned_cols=40 Identities=28% Similarity=0.422 Sum_probs=35.2
Q ss_pred CChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 85 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 85 ~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
+....|++.-..||-. .....++|..++||+|.||++|..
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 3456799999999987 888899999999999999999986
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=84.10 E-value=0.75 Score=31.38 Aligned_cols=40 Identities=20% Similarity=0.311 Sum_probs=27.8
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhcc
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 129 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~~ 129 (137)
.|+.++..+-- .-..|+++|-.+.+||+.|+.+|+.....
T Consensus 34 ~vr~~Lg~~~~-~e~~i~eal~~~~fDvekAl~~Ll~~~~~ 73 (79)
T PF08938_consen 34 QVREVLGDYVP-PEEQIKEALWHYYFDVEKALDYLLSKFKK 73 (79)
T ss_dssp CHHHHCCCCC---CCHHHHHHHHTTT-CCHHHHHHHHCCHS
T ss_pred HHHHHHcccCC-CHHHHHHHHHHHcCCHHHHHHHHHHhccC
Confidence 35555543322 56678899999999999999999976543
No 19
>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=83.37 E-value=2.2 Score=37.37 Aligned_cols=38 Identities=29% Similarity=0.403 Sum_probs=33.4
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 126 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~ 126 (137)
+..|+.+|.= | ++.+.|+.+|++.=+|.|.||+||+.-
T Consensus 157 e~~I~~i~eM-G-f~R~qV~~ALRAafNNPdRAVEYL~tG 194 (378)
T TIGR00601 157 ETTIEEIMEM-G-YEREEVERALRAAFNNPDRAVEYLLTG 194 (378)
T ss_pred HHHHHHHHHh-C-CCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence 5688888874 4 799999999999999999999999863
No 20
>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=82.81 E-value=2 Score=25.68 Aligned_cols=22 Identities=27% Similarity=0.525 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhCCCHHHHHHHH
Q 032619 102 SEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 102 ~~lIre~L~~~~gdvdaAI~~L 123 (137)
.+.|+++|+.++||+-.|...|
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 5789999999999999887765
No 21
>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=80.05 E-value=3.5 Score=36.11 Aligned_cols=43 Identities=26% Similarity=0.172 Sum_probs=39.5
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhccc
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 130 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~~~ 130 (137)
-+|..||..-|.+|.++..-+|.+..||+--||..|.+-+.+-
T Consensus 43 lavdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLLRAyRtTl 85 (358)
T PF05861_consen 43 LAVDRVMSEGSLYDPELAALAIKQARGDLIEAIFLLRAYRTTL 85 (358)
T ss_pred HHHHHHhccccccCHHHHHHHHHHhcCCHHHHHHHHHHHHhhc
Confidence 3688899999999999999999999999999999999987664
No 22
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=79.72 E-value=3.3 Score=35.95 Aligned_cols=45 Identities=22% Similarity=0.293 Sum_probs=38.4
Q ss_pred CChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhccc
Q 032619 85 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 130 (137)
Q Consensus 85 ~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~~~ 130 (137)
.....+++.-..||-+ +..++++|++|+||++.|.++|-...+.+
T Consensus 45 ~~~allk~LR~kTgas-~~ncKkALee~~gDl~~A~~~L~k~aqk~ 89 (340)
T KOG1071|consen 45 SSKALLKKLREKTGAS-MVNCKKALEECGGDLVLAEEWLHKKAQKE 89 (340)
T ss_pred ccHHHHHHHHHHcCCc-HHHHHHHHHHhCCcHHHHHHHHHHHHHHh
Confidence 3466888888999977 99999999999999999999997665544
No 23
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=76.05 E-value=4.6 Score=34.48 Aligned_cols=38 Identities=34% Similarity=0.723 Sum_probs=34.0
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
+.++.-||..|||. .+...+.|+++++++--||--++-
T Consensus 234 dRa~RIv~~aT~~~-~~~A~~~L~~~~~~vK~AIvm~~~ 271 (298)
T COG2103 234 DRAVRIVMEATGCS-AEEAEALLEEAGGNVKLAIVMLLT 271 (298)
T ss_pred HHHHHHHHHHhCCC-HHHHHHHHHHcCCccHhHHHHHHh
Confidence 56899999999997 888999999999999999977664
No 24
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=72.75 E-value=5.8 Score=32.34 Aligned_cols=36 Identities=31% Similarity=0.325 Sum_probs=30.3
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~L 123 (137)
..-|+.||.-.+|+.. .+.++|..++|||-.||..|
T Consensus 172 ~kDIeLVmsQanvSR~-kAVkALk~~~~DiVnAIM~L 207 (209)
T KOG2239|consen 172 AKDIELVMSQANVSRA-KAVKALKNNNNDIVNAIMEL 207 (209)
T ss_pred hhhHHHHHHHhhhhHH-HHHHHHHhccchHHHHHHHh
Confidence 4569999999999954 45559999999999999776
No 25
>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=70.38 E-value=7.4 Score=26.79 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=27.2
Q ss_pred HhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q 032619 94 MAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 127 (137)
Q Consensus 94 m~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~ 127 (137)
|..+|- +...|.++|..+.||+..|..|++..-
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 588899999999999999999888763
No 26
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=69.30 E-value=8.1 Score=32.38 Aligned_cols=38 Identities=26% Similarity=0.497 Sum_probs=32.8
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
.-++.-||..|||+ .+..+++|+.++|+|--||-.++.
T Consensus 236 ~ra~~i~~~~~~~~-~~~a~~~l~~~~~~vk~a~~~~~~ 273 (299)
T PRK05441 236 DRAVRIVMEATGVS-REEAEAALEAADGSVKLAIVMILT 273 (299)
T ss_pred HHHHHHHHHHHCcC-HHHHHHHHHHhCCCcHHHHHHHHh
Confidence 45788899999998 666889999999999999987765
No 27
>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=65.03 E-value=11 Score=31.54 Aligned_cols=38 Identities=26% Similarity=0.517 Sum_probs=32.7
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
.-++.-||..|||+ .+..+++|++++|+|--||--++.
T Consensus 231 ~Ra~~i~~~~~~~~-~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 231 ARAVRIVRQATDCN-KELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred HHHHHHHHHHhCcC-HHHHHHHHHHhCCCcHHHHHHHHh
Confidence 46788899999998 666899999999999999987654
No 28
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=62.88 E-value=13 Score=32.41 Aligned_cols=38 Identities=24% Similarity=0.395 Sum_probs=32.6
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 126 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~ 126 (137)
+..|.++|.- | +|.+.|+.+|++.=+|.|.||+|||--
T Consensus 136 e~~V~~Im~M-G-y~re~V~~AlRAafNNPeRAVEYLl~G 173 (340)
T KOG0011|consen 136 EQTVQQIMEM-G-YDREEVERALRAAFNNPERAVEYLLNG 173 (340)
T ss_pred HHHHHHHHHh-C-ccHHHHHHHHHHhhCChhhhHHHHhcC
Confidence 4578888863 3 899999999999999999999999853
No 29
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=61.38 E-value=5.9 Score=36.19 Aligned_cols=99 Identities=22% Similarity=0.344 Sum_probs=52.7
Q ss_pred eEEEEEecCCCcccccccCCCCCCCCCceeeecccc--h--hhhhhchhhhh----hhccCCCCCCCChhHHHHHHhcCC
Q 032619 27 RMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADA--D--ISAASIQSKTV----TSKLKGAAGIINAGSIKLVMAGSG 98 (137)
Q Consensus 27 ~~lhlaYh~geHYnSVR~~~d~~~~p~~p~~i~~d~--~--~~~~~~~~k~~----~~k~k~~~~~~~~~~v~~Vm~~TG 98 (137)
|++..|| ||-..-||.+-.++. |-+.+++...- . ...++...+.- +.+.+=..-.+.++.... +-+-|
T Consensus 239 kgf~~sy--Genl~Rl~~lKg~~s-pEraL~lRL~LLQGV~~yHqg~~deAye~le~a~~~l~elki~d~~lsl-lv~mG 314 (568)
T KOG2561|consen 239 KGFERSY--GENLSRLRSLKGGQS-PERALILRLELLQGVVAYHQGQRDEAYEALESAHAKLLELKINDETLSL-LVGMG 314 (568)
T ss_pred Hhhhhhh--hhhhHhhhhccCCCC-hhHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHeeccchHHHH-HHHcC
Confidence 4555555 677888888876653 55655543221 0 02222211100 000000001111223333 33445
Q ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHHhccc
Q 032619 99 CENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 130 (137)
Q Consensus 99 c~D~~lIre~L~~~~gdvdaAI~~Ll~~~~~~ 130 (137)
-. ....|-+|+.|+||||+||.||...++-.
T Consensus 315 fe-esdaRlaLRsc~g~Vd~AvqfI~erre~l 345 (568)
T KOG2561|consen 315 FE-ESDARLALRSCNGDVDSAVQFIIERREKL 345 (568)
T ss_pred CC-chHHHHHHHhccccHHHHHHHHHHHHHHH
Confidence 54 56678899999999999999998876544
No 30
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=61.30 E-value=10 Score=34.52 Aligned_cols=33 Identities=30% Similarity=0.457 Sum_probs=29.5
Q ss_pred HHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 93 VMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 93 Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
=.+.-|-.|.+.-.++|.+-+|||.+||+.||.
T Consensus 460 QL~~MGF~nre~nlqAL~atgGdi~aAverll~ 492 (493)
T KOG0010|consen 460 QLNDMGFLDREANLQALRATGGDINAAVERLLG 492 (493)
T ss_pred HHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence 345669999999999999999999999999984
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=57.52 E-value=12 Score=23.57 Aligned_cols=42 Identities=12% Similarity=0.102 Sum_probs=32.4
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhcccc
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 131 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~~~~ 131 (137)
.|.+++..||=. .+--+..|++++-|.+.|+...........
T Consensus 3 mv~~~s~~Tgmn-~~~s~~CL~~n~Wd~~~A~~~F~~l~~~~~ 44 (51)
T PF03943_consen 3 MVQQFSQQTGMN-LEWSQKCLEENNWDYERALQNFEELKAQGK 44 (51)
T ss_dssp HHHHHHHHCSS--CCHHHHHHHHTTT-CCHHHHHHHHCCCTT-
T ss_pred HHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHHHHcCC
Confidence 577888888875 667788999999999999999887765543
No 32
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=55.97 E-value=15 Score=22.84 Aligned_cols=28 Identities=25% Similarity=0.337 Sum_probs=23.2
Q ss_pred CChhHHHHHHhcCCCC-CHHHHHHHHHHh
Q 032619 85 INAGSIKLVMAGSGCE-NSEKVEEVLLQV 112 (137)
Q Consensus 85 ~~~~~v~~Vm~~TGc~-D~~lIre~L~~~ 112 (137)
+|++.++++|.-||.. ..++|.++|++.
T Consensus 7 iDd~Ll~eA~~l~g~~tk~~~V~~ALr~~ 35 (47)
T PF09957_consen 7 IDDELLAEAMRLTGTKTKKEAVNEALREL 35 (47)
T ss_pred eCHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence 4578999999999975 778888888875
No 33
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=55.46 E-value=20 Score=30.05 Aligned_cols=38 Identities=29% Similarity=0.629 Sum_probs=32.3
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
.-++.-||..|||+ .+..+++|++++|+|--||--++.
T Consensus 232 ~Ra~~i~~~~~~~~-~~~a~~~l~~~~~~vk~ai~~~~~ 269 (296)
T PRK12570 232 ARAVRIVMQATGCS-EDEAKELLKESDNDVKLAILMILT 269 (296)
T ss_pred HHHHHHHHHHHCcC-HHHHHHHHHHhCCccHHHHHHHHh
Confidence 45788899999997 666889999999999999987655
No 34
>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=53.76 E-value=58 Score=21.02 Aligned_cols=43 Identities=14% Similarity=0.101 Sum_probs=33.4
Q ss_pred ChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhc
Q 032619 86 NAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 128 (137)
Q Consensus 86 ~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~ 128 (137)
.++.+.++..-.-....+.|..-|+--+=|+.-||-.||.-+.
T Consensus 9 PedlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLsRDd 51 (53)
T PF11547_consen 9 PEDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLSRDD 51 (53)
T ss_dssp -HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHHHH-
T ss_pred CHHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhcccc
Confidence 3667777777776677899999999999999999999998654
No 35
>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=53.04 E-value=53 Score=21.68 Aligned_cols=42 Identities=14% Similarity=0.131 Sum_probs=35.5
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhcc
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 129 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~~ 129 (137)
...+.+++..||=. .+=-+..|++++.|.+.|+.....+...
T Consensus 13 ~~~v~~~~~~Tgmn-~~~s~~cLe~~~Wd~~~Al~~F~~lk~~ 54 (63)
T smart00804 13 QEMVQAFSAQTGMN-AEYSQMCLEDNNWDYERALKNFTELKSE 54 (63)
T ss_pred HHHHHHHHHHHCCC-HHHHHHHHHHcCCCHHHHHHHHHHHHhc
Confidence 45788899999976 7788889999999999999988876643
No 36
>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=49.70 E-value=8.7 Score=26.25 Aligned_cols=16 Identities=38% Similarity=0.688 Sum_probs=13.5
Q ss_pred EEEEecCCCccccccc
Q 032619 29 IHLSYHDGEHYNGVRL 44 (137)
Q Consensus 29 lhlaYh~geHYnSVR~ 44 (137)
--+.||.+.||+|+..
T Consensus 67 ~g~iy~t~dhy~tF~~ 82 (83)
T PF00545_consen 67 CGVIYHTGDHYNTFVR 82 (83)
T ss_dssp EEEEEECSSTTSSEEE
T ss_pred CCeEEEcCCchhceEe
Confidence 4577999999999875
No 37
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=49.24 E-value=23 Score=26.36 Aligned_cols=41 Identities=24% Similarity=0.281 Sum_probs=33.3
Q ss_pred CCChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 84 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 84 ~~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
.+....++.||+..-.+ ...++..|+...||+-+|...|+.
T Consensus 78 ~IkkeDlelImnELei~-k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 78 TIKKEDLELIMNELEIS-KAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred ccCHHHHHHHHHHHHHH-HHHHHHHHHHhcccHHHHHHHHhc
Confidence 34466789999977665 677888999999999999988864
No 38
>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=46.22 E-value=13 Score=30.30 Aligned_cols=33 Identities=39% Similarity=0.671 Sum_probs=28.3
Q ss_pred hhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAI 120 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI 120 (137)
.-++.-||..|||+ .+..+++|+..+|++-.||
T Consensus 223 ~ra~~i~~~~~~~~-~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 223 ERAIRIVMEATGVS-RDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHHHCcC-HHHHHHHHHHhCCCceeee
Confidence 45788899999998 6668899999999998776
No 39
>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=46.09 E-value=58 Score=20.86 Aligned_cols=37 Identities=19% Similarity=0.277 Sum_probs=31.0
Q ss_pred ChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHH
Q 032619 86 NAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 86 ~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~L 123 (137)
++..|+..+...||+ .+.++++.+..+.++.+.-.+|
T Consensus 19 e~~ev~ywa~~~gvt-~~~L~~AV~~vG~~~~~V~~~L 55 (57)
T PF12244_consen 19 EPYEVRYWAKRFGVT-EEQLREAVRAVGNSRAAVRAYL 55 (57)
T ss_pred CHHHHHHHHHHHCcC-HHHHHHHHHHHCcCHHHHHHHH
Confidence 367899999999999 7778889999998887766665
No 40
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=45.86 E-value=38 Score=29.75 Aligned_cols=40 Identities=18% Similarity=0.174 Sum_probs=34.4
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 127 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~ 127 (137)
..|.++|.-|+=.+++..++.|..+++|+++||-.++...
T Consensus 8 ~lv~~fl~It~~~t~e~A~q~L~~~~~~le~ai~Lffe~~ 47 (356)
T KOG1364|consen 8 ALVSKFLAITVQQTVEIATQYLSAADWDLEAAINLFFEHG 47 (356)
T ss_pred HHHHHHHHHhccccHHHHHHHHHhcCCcHHHHHHHHHHhc
Confidence 4799999999955699999999999999999997666543
No 41
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=44.17 E-value=71 Score=20.60 Aligned_cols=35 Identities=20% Similarity=0.293 Sum_probs=28.3
Q ss_pred HHHHhcCCCC-CHHHHHHHHHHhCCCHHHHHHHHHH
Q 032619 91 KLVMAGSGCE-NSEKVEEVLLQVGGDVDAAIEFLIA 125 (137)
Q Consensus 91 ~~Vm~~TGc~-D~~lIre~L~~~~gdvdaAI~~Ll~ 125 (137)
.+-..++||. ++.+.++.|.+.+=+.++.++.|-+
T Consensus 6 ~~~l~~~~CdHtlr~t~~fl~~~~~~~~~vl~~l~~ 41 (53)
T PF10905_consen 6 DEKLSAFGCDHTLRLTRQFLRQRQLDWEDVLEWLRE 41 (53)
T ss_pred HhHcCcCCCCCcHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3445678997 9999999999999999887777654
No 42
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=41.57 E-value=31 Score=33.37 Aligned_cols=30 Identities=33% Similarity=0.474 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q 032619 98 GCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 127 (137)
Q Consensus 98 Gc~D~~lIre~L~~~~gdvdaAI~~Ll~~~ 127 (137)
|.++.++.--.|.+..|||..|++-||--.
T Consensus 573 gGtN~ElALH~L~EakGnv~vAlE~LLlr~ 602 (907)
T KOG4167|consen 573 GGTNSELALHSLFEAKGNVMVALEMLLLRK 602 (907)
T ss_pred CCccHHHHHHHHHHhcccHHHHHHHHHhcC
Confidence 557999999999999999999999998644
No 43
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=41.52 E-value=38 Score=20.41 Aligned_cols=25 Identities=32% Similarity=0.627 Sum_probs=19.0
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHHh
Q 032619 101 NSEKVEEVLLQVGGDVDAAIEFLIAEQ 127 (137)
Q Consensus 101 D~~lIre~L~~~~gdvdaAI~~Ll~~~ 127 (137)
+...|++.+. .||++.|+..+-...
T Consensus 4 ~~~~i~~~i~--~g~~~~a~~~~~~~~ 28 (58)
T smart00668 4 ERKRIRELIL--KGDWDEALEWLSSLK 28 (58)
T ss_pred HHHHHHHHHH--cCCHHHHHHHHHHcC
Confidence 4567777776 799999999885544
No 44
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=40.83 E-value=47 Score=28.78 Aligned_cols=42 Identities=29% Similarity=0.230 Sum_probs=38.2
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhccc
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 130 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~~~ 130 (137)
+|..||..-+.+|.++.-=+|.+..||+-.||..|.+-+.+-
T Consensus 44 aVdRVM~EgslyDreLAALAikQa~GD~~EAIFLlRAYRTTL 85 (367)
T COG3626 44 AVDRVMTEGSLYDRELAALALKQASGDLVEAIFLLRAYRTTL 85 (367)
T ss_pred HHHHHhhccchhHHHHHHHHHHHhcchHHHHHHHHHHHHhcc
Confidence 688999999999999999999999999999999998877653
No 45
>KOG2934 consensus Uncharacterized conserved protein, contains Josephin domain [General function prediction only]
Probab=40.01 E-value=22 Score=28.71 Aligned_cols=22 Identities=23% Similarity=0.294 Sum_probs=20.0
Q ss_pred HhcCCCCCHHHHHHHHHHhCCC
Q 032619 94 MAGSGCENSEKVEEVLLQVGGD 115 (137)
Q Consensus 94 m~~TGc~D~~lIre~L~~~~gd 115 (137)
|-++||+|+.-|-.+|+.++.-
T Consensus 75 ~~g~Gnydvnvimaalq~~gl~ 96 (204)
T KOG2934|consen 75 WKGPGNYDVNVIMAALQQCGLE 96 (204)
T ss_pred ccCCCcccHHHHHHHHHhcCce
Confidence 5699999999999999999875
No 46
>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=39.67 E-value=58 Score=19.94 Aligned_cols=28 Identities=18% Similarity=0.141 Sum_probs=20.1
Q ss_pred cCCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 032619 96 GSGCENSEKVEEVLLQVGGDVDAAIEFLI 124 (137)
Q Consensus 96 ~TGc~D~~lIre~L~~~~gdvdaAI~~Ll 124 (137)
...|.| ..+..-|++-++||+.|+.-|.
T Consensus 26 ~~~~~d-~~llRFLRARkf~v~~A~~mL~ 53 (55)
T PF03765_consen 26 KEDHDD-NFLLRFLRARKFDVEKAFKMLK 53 (55)
T ss_dssp TSS-SH-HHHHHHHHHTTT-HHHHHHHHH
T ss_pred cCCCCH-HHHHHHHHHccCCHHHHHHHHH
Confidence 334556 5555699999999999998775
No 47
>COG4290 Guanyl-specific ribonuclease Sa [Nucleotide transport and metabolism]
Probab=33.63 E-value=15 Score=28.43 Aligned_cols=15 Identities=33% Similarity=0.643 Sum_probs=13.2
Q ss_pred ecCCCcccccccCCC
Q 032619 33 YHDGEHYNGVRLKED 47 (137)
Q Consensus 33 Yh~geHYnSVR~~~d 47 (137)
|--.+||+|+|++.+
T Consensus 138 YYT~dHY~SFrri~~ 152 (152)
T COG4290 138 YYTSDHYESFRRITD 152 (152)
T ss_pred EEecchhhhhhcccC
Confidence 888999999999864
No 48
>PRK01905 DNA-binding protein Fis; Provisional
Probab=32.60 E-value=67 Score=21.43 Aligned_cols=23 Identities=35% Similarity=0.517 Sum_probs=19.1
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHH
Q 032619 101 NSEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 101 D~~lIre~L~~~~gdvdaAI~~L 123 (137)
..+.|+++|+.++||+-.|...|
T Consensus 38 E~~~i~~aL~~~~gn~s~aAr~L 60 (77)
T PRK01905 38 EKPLLEVVMEQAGGNQSLAAEYL 60 (77)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH
Confidence 46789999999999998886544
No 49
>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]
Probab=32.46 E-value=1e+02 Score=23.85 Aligned_cols=45 Identities=16% Similarity=0.090 Sum_probs=35.5
Q ss_pred CCCChhHHHHHHhcCCCC----CHHHHHHHHHHhC--CCHHHHHHHHHHHh
Q 032619 83 GIINAGSIKLVMAGSGCE----NSEKVEEVLLQVG--GDVDAAIEFLIAEQ 127 (137)
Q Consensus 83 ~~~~~~~v~~Vm~~TGc~----D~~lIre~L~~~~--gdvdaAI~~Ll~~~ 127 (137)
..+|-|.+++.|+-.=-+ +...|.++|++|+ +|+-.||-.|-+..
T Consensus 61 ~~iD~wEvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK 111 (149)
T KOG4077|consen 61 PEIDGWEVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIK 111 (149)
T ss_pred ccchHHHHHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence 455678899999854333 5688999999999 99999998887654
No 50
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=31.90 E-value=47 Score=22.99 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=22.6
Q ss_pred CcceeEEEEeCC--CcceEEeec----cCCCceEEEEEecC
Q 032619 1 MYCLLLSLMQHM--SPRWYIRNF----DYHEARMIHLSYHD 35 (137)
Q Consensus 1 ~~~~~i~Ihq~~--~p~w~I~~~----~~~~~~~lhlaYh~ 35 (137)
+|+++|+|++.. .+.+.+... +....+.|+|.|+.
T Consensus 72 ~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~~~~ 112 (121)
T PF02338_consen 72 VLNRPIIVYSSSDGDNVVFIKFTGKYPPLESPPPICLCYHG 112 (121)
T ss_dssp HHTSEEEEECETTTBEEEEEEESCEESTTTTTTSEEEEEET
T ss_pred HhCCeEEEEEcCCCCccceeeecCccccCCCCCeEEEEEcC
Confidence 478999998753 444555432 23355789998874
No 51
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=31.48 E-value=1e+02 Score=22.59 Aligned_cols=43 Identities=16% Similarity=0.119 Sum_probs=34.8
Q ss_pred CChhHHHHHHhcCCCC----CHHHHHHHHHHhC--CCHHHHHHHHHHHh
Q 032619 85 INAGSIKLVMAGSGCE----NSEKVEEVLLQVG--GDVDAAIEFLIAEQ 127 (137)
Q Consensus 85 ~~~~~v~~Vm~~TGc~----D~~lIre~L~~~~--gdvdaAI~~Ll~~~ 127 (137)
+|-+.+++.||-.-.. +...|..+|++|+ +|.-.||-+|-+..
T Consensus 21 iD~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK 69 (103)
T cd00923 21 IDGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIK 69 (103)
T ss_pred ccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 4667888888866554 6788999999999 89999998887665
No 52
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=30.01 E-value=82 Score=26.36 Aligned_cols=33 Identities=21% Similarity=0.364 Sum_probs=27.4
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHH
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEF 122 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~ 122 (137)
.+..+|..+||. .+..++.|...+|++-.|+..
T Consensus 265 k~a~~~~~~~~~-~~~a~~~l~~~~g~~~~~~~~ 297 (299)
T PRK05441 265 KLAIVMILTGLD-AAEAKALLARHGGFLRKALAE 297 (299)
T ss_pred HHHHHHHHhCCC-HHHHHHHHHHcCCCHHHHHhh
Confidence 355677788886 888999999999999999864
No 53
>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=28.13 E-value=1.2e+02 Score=26.65 Aligned_cols=38 Identities=16% Similarity=0.239 Sum_probs=31.8
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHh
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 127 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~ 127 (137)
++|+..|.- | .+..+|.|+..+|+-|-+.|..|||...
T Consensus 339 ~AIeRL~~L-G-F~r~~viqaY~ACdKNEelAAn~Lf~~~ 376 (378)
T TIGR00601 339 EAIERLCAL-G-FDRGLVIQAYFACDKNEELAANYLLSQN 376 (378)
T ss_pred HHHHHHHHc-C-CCHHHHHHHHHhcCCcHHHHHHHHHhhc
Confidence 466666653 5 7899999999999999999999999753
No 54
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=27.93 E-value=84 Score=22.10 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=19.3
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHH
Q 032619 101 NSEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 101 D~~lIre~L~~~~gdvdaAI~~L 123 (137)
....|+++|+.++||+..|...|
T Consensus 56 Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 56 EAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHh
Confidence 46789999999999999887654
No 55
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=26.81 E-value=1.5e+02 Score=21.92 Aligned_cols=45 Identities=13% Similarity=0.070 Sum_probs=33.2
Q ss_pred CCChhHHHHHHhcCCCC----CHHHHHHHHHHhC--CCHHHHHHHHHHHhc
Q 032619 84 IINAGSIKLVMAGSGCE----NSEKVEEVLLQVG--GDVDAAIEFLIAEQG 128 (137)
Q Consensus 84 ~~~~~~v~~Vm~~TGc~----D~~lIre~L~~~~--gdvdaAI~~Ll~~~~ 128 (137)
.+|-+.+++-|+-.-.. +...|..+|.+|+ +|.-.||-+|-+...
T Consensus 23 ~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~ 73 (108)
T PF02284_consen 23 DIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKD 73 (108)
T ss_dssp T--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence 34567888888876554 5788999999999 999999998877653
No 56
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=26.46 E-value=78 Score=19.16 Aligned_cols=25 Identities=20% Similarity=0.237 Sum_probs=20.5
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHh
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQV 112 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~ 112 (137)
.....+...||+.-..+|+++|++.
T Consensus 15 ~~L~~ls~~t~i~~S~Ll~eAle~~ 39 (44)
T PF12651_consen 15 EKLKELSEETGIPKSKLLREALEDY 39 (44)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3567777899999999999998764
No 57
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=25.41 E-value=35 Score=29.98 Aligned_cols=116 Identities=12% Similarity=0.006 Sum_probs=58.8
Q ss_pred EEEEeCCCcceEEeeccCC-CceEEEEEecCCCcccccccCCCCCCCCCceeeecccchhhhhhchhhh--hhhccCCCC
Q 032619 6 LSLMQHMSPRWYIRNFDYH-EARMIHLSYHDGEHYNGVRLKEDSCIGSARPIIIKADADISAASIQSKT--VTSKLKGAA 82 (137)
Q Consensus 6 i~Ihq~~~p~w~I~~~~~~-~~~~lhlaYh~geHYnSVR~~~d~~~~p~~p~~i~~d~~~~~~~~~~k~--~~~k~k~~~ 82 (137)
+..|-.+.|.|.+.++.+. ...+.+.+||.| |++..+.-..-+..+..+.+.....-+.....+.+. ..++.+
T Consensus 138 ~~~~~~~~~~~~~~~~sd~~~~~~~~~~~~~~-~~~~~~~g~~in~y~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~--- 213 (371)
T KOG2605|consen 138 DLEVERNSPEWLGQSPSDPLRSVPSMEAIHAR-HPEAKEVGVRINDYNPKVLVPFINGLPPSEEEPQSAHERSAKRK--- 213 (371)
T ss_pred chhhhccCchhccccccccccccccccchhhc-cccchhhcccccCCCccccccccccCCCchHHHHHHHHHHHHHH---
Confidence 4455667899999986544 468899999987 777666544434444344332222222111111000 000000
Q ss_pred CCCChhHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhc
Q 032619 83 GIINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 128 (137)
Q Consensus 83 ~~~~~~~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~~Ll~~~~ 128 (137)
..+.....+-++.+. |....+.-|+.. +.+....++.+...+.
T Consensus 214 ~~~g~e~~Kv~edGs-C~fra~aDQvy~--d~e~~~~~~~~~~dq~ 256 (371)
T KOG2605|consen 214 KHFGFEYKKVVEDGS-CLFRALADQVYG--DDEQHDHNRRECVDQL 256 (371)
T ss_pred HHhhhhhhhcccCCc-hhhhccHHHhhc--CHHHHHHHHHHHHHHH
Confidence 011121222222333 333355555555 7778888888877765
No 58
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=24.84 E-value=1.1e+02 Score=25.68 Aligned_cols=32 Identities=25% Similarity=0.390 Sum_probs=27.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHH
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIE 121 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~ 121 (137)
.+..+|..+||+ .+..++.|..++|++..|++
T Consensus 261 k~ai~~~~~~~~-~~~a~~~l~~~~~~~~~~l~ 292 (296)
T PRK12570 261 KLAILMILTGMD-VEQARAALSHADGFLRKAIE 292 (296)
T ss_pred HHHHHHHHhCCC-HHHHHHHHHHcCChHHHHHH
Confidence 355677788886 88899999999999999986
No 59
>PHA00617 ribbon-helix-helix domain containing protein
Probab=24.46 E-value=1.7e+02 Score=20.32 Aligned_cols=25 Identities=20% Similarity=0.162 Sum_probs=21.7
Q ss_pred hHHHHHHhcCCCCCHHHHHHHHHHh
Q 032619 88 GSIKLVMAGSGCENSEKVEEVLLQV 112 (137)
Q Consensus 88 ~~v~~Vm~~TGc~D~~lIre~L~~~ 112 (137)
..+...+..+|++....|+++|++.
T Consensus 52 erLD~LA~~~GrsRSelIreAI~~Y 76 (80)
T PHA00617 52 AKLEQVAIKMKKSKSEIIREALEKY 76 (80)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 4678888899999999999999875
No 60
>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=24.38 E-value=93 Score=26.03 Aligned_cols=32 Identities=22% Similarity=0.300 Sum_probs=26.4
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHH
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIE 121 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~~~gdvdaAI~ 121 (137)
.+..+|..+||. .+..++.|..++|++-.|++
T Consensus 260 k~Ai~~~~~~~~-~~~a~~~l~~~~g~~~~~l~ 291 (291)
T TIGR00274 260 KLAIVMILSTLS-ASEAKVLLDRHGGFLRQALD 291 (291)
T ss_pred HHHHHHHHhCCC-HHHHHHHHHHcCCcHHHhhC
Confidence 355677888886 78899999999999998874
No 61
>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=23.70 E-value=66 Score=20.31 Aligned_cols=21 Identities=19% Similarity=0.455 Sum_probs=17.2
Q ss_pred hhHHHHHHhcCCCCCHHHHHH
Q 032619 87 AGSIKLVMAGSGCENSEKVEE 107 (137)
Q Consensus 87 ~~~v~~Vm~~TGc~D~~lIre 107 (137)
+..++-.|++.||.|..+|-.
T Consensus 12 eqIvema~nG~GiRdtaRvL~ 32 (46)
T PF12759_consen 12 EQIVEMAFNGSGIRDTARVLK 32 (46)
T ss_pred HHHHHHHhcCCcchhhHhHhc
Confidence 567889999999998887643
No 62
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=21.04 E-value=1.1e+02 Score=26.30 Aligned_cols=22 Identities=18% Similarity=0.237 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhCCCHHHHHHHH
Q 032619 102 SEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 102 ~~lIre~L~~~~gdvdaAI~~L 123 (137)
.++|.++|+.++||+..|...|
T Consensus 431 ~~~i~~aL~~~~gn~~~aA~~L 452 (469)
T PRK10923 431 RTLLTTALRHTQGHKQEAARLL 452 (469)
T ss_pred HHHHHHHHHHhCCCHHHHHHHh
Confidence 4569999999999999887765
No 63
>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=20.99 E-value=1e+02 Score=20.13 Aligned_cols=23 Identities=13% Similarity=0.284 Sum_probs=18.7
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHH
Q 032619 89 SIKLVMAGSGCENSEKVEEVLLQ 111 (137)
Q Consensus 89 ~v~~Vm~~TGc~D~~lIre~L~~ 111 (137)
++.+|+.+.|+.+...|.+.|..
T Consensus 27 t~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 27 TVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp -HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CHHHHHHHhCCCChHHHHHHHHH
Confidence 79999999999988888876654
No 64
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=20.48 E-value=1.1e+02 Score=25.75 Aligned_cols=22 Identities=23% Similarity=0.223 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhCCCHHHHHHHH
Q 032619 102 SEKVEEVLLQVGGDVDAAIEFL 123 (137)
Q Consensus 102 ~~lIre~L~~~~gdvdaAI~~L 123 (137)
...|+++|+.++||+-.|...|
T Consensus 294 ~~~I~~aL~~~~gn~~~aA~~L 315 (329)
T TIGR02974 294 IELLQQALAEAQFNQRKAAELL 315 (329)
T ss_pred HHHHHHHHHHhCCCHHHHHHHh
Confidence 5689999999999999998765
Done!