Query 029636
Match_columns 190
No_of_seqs 147 out of 173
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 16:05:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029636.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029636hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00397 WW: WW domain; Inter 99.0 1E-10 2.2E-15 72.2 2.2 31 62-92 1-31 (31)
2 smart00456 WW Domain with 2 co 98.8 2E-09 4.3E-14 65.4 2.6 31 62-93 1-31 (32)
3 cd00201 WW Two conserved trypt 98.7 1.2E-08 2.5E-13 61.0 2.6 30 63-93 1-30 (31)
4 KOG3259 Peptidyl-prolyl cis-tr 98.2 4.5E-07 9.8E-12 75.3 1.9 36 59-94 4-39 (163)
5 KOG1891 Proline binding protei 97.3 0.00018 4E-09 63.7 3.3 64 21-93 83-159 (271)
6 KOG1891 Proline binding protei 96.6 0.0022 4.8E-08 57.0 4.1 40 58-98 90-129 (271)
7 COG5104 PRP40 Splicing factor 96.3 0.0017 3.7E-08 62.3 1.8 61 31-95 22-86 (590)
8 COG5104 PRP40 Splicing factor 95.4 0.007 1.5E-07 58.2 1.5 30 64-94 15-44 (590)
9 KOG3209 WW domain-containing p 93.9 0.033 7.2E-07 56.3 2.2 34 59-93 220-253 (984)
10 KOG0940 Ubiquitin protein liga 90.3 0.19 4.1E-06 46.5 2.4 58 35-95 77-146 (358)
11 PRK08351 DNA-directed RNA poly 89.5 0.16 3.4E-06 36.6 0.9 25 134-162 1-25 (61)
12 cd00201 WW Two conserved trypt 87.9 0.4 8.6E-06 28.1 1.8 16 34-49 12-30 (31)
13 PF00397 WW: WW domain; Inter 86.8 0.41 8.8E-06 29.2 1.4 16 33-48 13-31 (31)
14 smart00391 MBD Methyl-CpG bind 83.6 0.65 1.4E-05 34.1 1.5 25 58-82 4-35 (77)
15 cd00122 MBD MeCP2, MBD1, MBD2, 83.0 1 2.2E-05 31.3 2.2 26 58-83 2-33 (62)
16 PRK06393 rpoE DNA-directed RNA 82.7 0.46 1E-05 34.6 0.4 24 135-162 4-27 (64)
17 KOG3209 WW domain-containing p 80.4 1.2 2.7E-05 45.6 2.5 62 31-93 232-299 (984)
18 PRK00398 rpoP DNA-directed RNA 77.6 1.9 4.1E-05 28.2 2.0 34 134-167 1-36 (46)
19 TIGR02098 MJ0042_CXXC MJ0042 f 69.4 3 6.4E-05 26.0 1.3 26 137-162 3-35 (38)
20 COG3357 Predicted transcriptio 66.9 2.4 5.2E-05 33.2 0.6 32 132-163 54-87 (97)
21 cd01397 HAT_MBD Methyl-CpG bin 66.4 4 8.6E-05 30.3 1.7 24 58-81 2-31 (73)
22 PF09538 FYDLN_acid: Protein o 66.0 5 0.00011 31.5 2.3 27 138-165 11-39 (108)
23 KOG0940 Ubiquitin protein liga 65.4 5.5 0.00012 37.0 2.8 47 48-94 46-96 (358)
24 PF01429 MBD: Methyl-CpG bindi 64.3 3.7 8.1E-05 29.7 1.2 29 58-87 7-42 (77)
25 TIGR00100 hypA hydrogenase nic 60.5 7 0.00015 30.4 2.2 29 134-162 68-96 (115)
26 PF07295 DUF1451: Protein of u 58.3 9.6 0.00021 31.3 2.7 36 127-162 103-140 (146)
27 PRK03681 hypA hydrogenase nick 58.2 8 0.00017 30.1 2.1 29 134-162 68-97 (114)
28 PRK12380 hydrogenase nickel in 57.9 8.6 0.00019 29.9 2.3 28 134-161 68-95 (113)
29 TIGR00155 pqiA_fam integral me 57.3 5.5 0.00012 37.2 1.3 27 136-163 215-241 (403)
30 PF12172 DUF35_N: Rubredoxin-l 56.9 7.5 0.00016 24.2 1.5 28 132-161 7-34 (37)
31 COG1675 TFA1 Transcription ini 56.7 4.1 8.9E-05 34.6 0.3 30 135-164 112-144 (176)
32 PF13719 zinc_ribbon_5: zinc-r 56.3 4.4 9.6E-05 25.7 0.4 25 137-161 3-34 (37)
33 PRK13130 H/ACA RNA-protein com 55.7 15 0.00032 26.0 3.0 29 135-167 4-32 (56)
34 KOG0155 Transcription factor C 54.8 9 0.0002 38.1 2.3 35 59-94 108-143 (617)
35 COG2260 Predicted Zn-ribbon RN 53.2 15 0.00033 26.5 2.7 28 136-167 5-32 (59)
36 PRK15103 paraquat-inducible me 51.7 7.7 0.00017 36.5 1.3 26 136-163 221-246 (419)
37 PF01155 HypA: Hydrogenase exp 50.9 5.8 0.00013 30.6 0.3 29 134-162 68-96 (113)
38 PF11023 DUF2614: Protein of u 50.7 8.6 0.00019 31.0 1.3 34 134-168 67-101 (114)
39 smart00661 RPOL9 RNA polymeras 50.6 11 0.00024 24.4 1.6 28 138-165 2-33 (52)
40 COG1096 Predicted RNA-binding 50.4 9.5 0.00021 33.0 1.6 33 130-162 143-175 (188)
41 cd04482 RPA2_OBF_like RPA2_OBF 50.3 8.1 0.00018 28.7 1.0 11 149-159 81-91 (91)
42 PF10122 Mu-like_Com: Mu-like 47.7 7.8 0.00017 27.2 0.5 31 137-167 5-39 (51)
43 PF10571 UPF0547: Uncharacteri 47.2 11 0.00023 22.7 1.0 20 139-160 3-22 (26)
44 KOG3259 Peptidyl-prolyl cis-tr 46.7 11 0.00025 31.8 1.5 23 31-53 17-42 (163)
45 TIGR02300 FYDLN_acid conserved 45.3 17 0.00036 29.9 2.1 29 138-166 11-40 (129)
46 PRK03824 hypA hydrogenase nick 44.0 21 0.00047 28.5 2.6 29 134-162 68-117 (135)
47 PF10164 DUF2367: Uncharacteri 44.0 18 0.0004 28.4 2.1 17 131-147 44-60 (98)
48 PRK00420 hypothetical protein; 42.9 12 0.00025 29.8 0.9 35 131-165 18-53 (112)
49 COG4416 Com Mu-like prophage p 42.4 10 0.00022 27.3 0.5 11 153-163 25-35 (60)
50 PRK00564 hypA hydrogenase nick 41.9 15 0.00033 28.6 1.4 29 134-162 69-98 (117)
51 KOG4334 Uncharacterized conser 41.9 17 0.00036 36.2 2.0 39 54-93 147-185 (650)
52 PRK11032 hypothetical protein; 41.9 24 0.00051 29.6 2.6 35 128-162 116-152 (160)
53 cd00350 rubredoxin_like Rubred 41.3 19 0.00042 22.2 1.6 23 138-160 3-25 (33)
54 PF03604 DNA_RNApol_7kD: DNA d 40.9 14 0.0003 23.3 0.8 25 138-162 2-27 (32)
55 TIGR00373 conserved hypothetic 40.5 14 0.00031 30.1 1.1 28 135-162 108-138 (158)
56 PF08274 PhnA_Zn_Ribbon: PhnA 40.4 11 0.00024 23.5 0.4 12 152-163 2-13 (30)
57 KOG3552 FERM domain protein FR 39.8 9.7 0.00021 40.4 0.0 32 59-91 17-48 (1298)
58 KOG4286 Dystrophin-like protei 37.8 12 0.00025 38.9 0.2 28 65-93 353-380 (966)
59 PF14369 zf-RING_3: zinc-finge 37.1 31 0.00066 21.9 2.0 22 139-160 5-29 (35)
60 COG1867 TRM1 N2,N2-dimethylgua 37.0 18 0.0004 34.3 1.4 31 134-164 238-269 (380)
61 KOG0155 Transcription factor C 36.9 20 0.00043 35.7 1.6 31 63-94 11-41 (617)
62 COG2093 DNA-directed RNA polym 36.7 11 0.00025 27.5 -0.0 26 134-161 2-27 (64)
63 PF03682 UPF0158: Uncharacteri 36.5 19 0.00041 29.8 1.2 17 65-81 21-37 (163)
64 PRK06266 transcription initiat 35.6 22 0.00047 29.8 1.4 30 135-164 116-148 (178)
65 PF10058 DUF2296: Predicted in 35.5 29 0.00063 24.1 1.8 30 132-161 18-53 (54)
66 PF11238 DUF3039: Protein of u 35.4 22 0.00048 25.6 1.3 32 131-162 23-54 (58)
67 smart00659 RPOLCX RNA polymera 35.4 27 0.00059 23.2 1.6 29 136-164 2-31 (44)
68 cd01396 MeCP2_MBD MeCP2, MBD1, 35.1 27 0.00058 25.7 1.7 24 60-83 5-34 (77)
69 COG1579 Zn-ribbon protein, pos 34.9 13 0.00028 33.0 0.0 27 137-163 198-232 (239)
70 cd07973 Spt4 Transcription elo 34.4 22 0.00047 27.6 1.2 26 137-162 4-30 (98)
71 COG5242 TFB4 RNA polymerase II 33.9 27 0.00058 31.8 1.8 28 134-163 258-285 (296)
72 COG0375 HybF Zn finger protein 33.7 22 0.00048 28.5 1.1 30 134-163 68-97 (115)
73 PF13248 zf-ribbon_3: zinc-rib 32.8 21 0.00045 21.0 0.7 21 138-160 4-24 (26)
74 PF06943 zf-LSD1: LSD1 zinc fi 30.9 35 0.00075 20.7 1.4 23 139-161 1-25 (25)
75 COG0846 SIR2 NAD-dependent pro 30.7 36 0.00078 30.2 2.1 31 132-162 118-157 (250)
76 TIGR01384 TFS_arch transcripti 29.6 22 0.00048 26.4 0.5 27 138-164 2-28 (104)
77 TIGR00155 pqiA_fam integral me 29.1 39 0.00085 31.7 2.1 28 136-163 13-44 (403)
78 COG2995 PqiA Uncharacterized p 28.4 27 0.00059 33.6 1.0 29 134-163 218-246 (418)
79 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.1 45 0.00097 26.5 2.1 30 133-162 31-61 (166)
80 PRK02935 hypothetical protein; 27.7 43 0.00093 26.9 1.8 36 132-168 66-102 (110)
81 smart00564 PQQ beta-propeller 27.2 49 0.0011 18.9 1.6 18 74-91 15-32 (33)
82 COG2995 PqiA Uncharacterized p 26.7 39 0.00085 32.5 1.7 31 133-163 15-49 (418)
83 PF15232 DUF4585: Domain of un 26.5 41 0.00089 25.4 1.5 29 69-97 11-41 (75)
84 PRK05743 ileS isoleucyl-tRNA s 26.4 20 0.00044 36.7 -0.3 25 138-162 882-910 (912)
85 PF11008 DUF2846: Protein of u 26.2 61 0.0013 24.6 2.4 20 65-84 84-103 (117)
86 KOG0150 Spliceosomal protein F 25.8 69 0.0015 30.1 3.1 29 65-94 152-180 (336)
87 TIGR02605 CxxC_CxxC_SSSS putat 25.8 54 0.0012 21.4 1.8 25 136-160 5-34 (52)
88 cd01412 SIRT5_Af1_CobB SIRT5_A 25.6 41 0.00088 28.2 1.5 27 136-162 109-140 (224)
89 PLN02843 isoleucyl-tRNA synthe 25.5 30 0.00064 36.0 0.7 26 138-163 934-963 (974)
90 PF14949 ARF7EP_C: ARF7 effect 25.0 37 0.0008 26.7 1.0 17 136-161 67-83 (103)
91 PRK15103 paraquat-inducible me 24.7 51 0.0011 31.1 2.1 28 137-164 11-42 (419)
92 KOG3352 Cytochrome c oxidase, 24.6 89 0.0019 26.4 3.2 35 132-167 107-148 (153)
93 PF02309 AUX_IAA: AUX/IAA fami 23.9 26 0.00056 29.6 0.0 37 3-39 3-39 (215)
94 PRK00432 30S ribosomal protein 23.3 38 0.00082 23.1 0.7 28 134-161 18-46 (50)
95 PRK13804 ileS isoleucyl-tRNA s 23.0 22 0.00048 36.8 -0.7 26 138-163 924-953 (961)
96 PF14435 SUKH-4: SUKH-4 immuni 22.7 51 0.0011 26.3 1.5 20 65-84 86-105 (179)
97 cd01411 SIR2H SIR2H: Uncharact 22.4 54 0.0012 27.9 1.6 29 134-162 116-146 (225)
98 PF03811 Zn_Tnp_IS1: InsA N-te 21.6 54 0.0012 21.1 1.1 14 149-162 2-15 (36)
99 TIGR01053 LSD1 zinc finger dom 21.3 71 0.0015 19.9 1.6 26 137-162 2-29 (31)
100 PF09003 Phage_integ_N: Bacter 21.1 50 0.0011 24.7 1.0 20 61-80 11-30 (75)
101 PRK12496 hypothetical protein; 21.0 53 0.0011 27.1 1.3 26 137-162 128-153 (164)
102 PF09723 Zn-ribbon_8: Zinc rib 20.8 91 0.002 20.1 2.1 24 137-160 6-34 (42)
103 PF02150 RNA_POL_M_15KD: RNA p 20.7 32 0.0007 21.7 -0.1 28 138-165 3-33 (35)
104 PF13453 zf-TFIIB: Transcripti 20.6 47 0.001 21.1 0.7 8 154-161 1-8 (41)
105 PF02701 zf-Dof: Dof domain, z 20.3 60 0.0013 23.8 1.3 13 150-162 3-15 (63)
106 PF06677 Auto_anti-p27: Sjogre 20.3 55 0.0012 21.6 1.0 29 131-159 12-41 (41)
No 1
>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....
Probab=99.04 E-value=1e-10 Score=72.16 Aligned_cols=31 Identities=42% Similarity=0.999 Sum_probs=29.5
Q ss_pred CCccchhcccCCCcceEEeecCCCCccccCC
Q 029636 62 LPLDWERCLDLQSGRMYYFNRKSSKKSWSLP 92 (190)
Q Consensus 62 LPsgWEq~LDlkSG~iYY~N~~T~~ssw~dP 92 (190)
||.||+++.|.++|++||+|..|++++|++|
T Consensus 1 LP~gW~~~~~~~~g~~YY~N~~t~~s~W~~P 31 (31)
T PF00397_consen 1 LPPGWEEYFDPDSGRPYYYNHETGESQWERP 31 (31)
T ss_dssp SSTTEEEEEETTTSEEEEEETTTTEEESSST
T ss_pred CCcCCEEEEcCCCCCEEEEeCCCCCEEeCCC
Confidence 7999999998768999999999999999998
No 2
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=98.84 E-value=2e-09 Score=65.36 Aligned_cols=31 Identities=39% Similarity=0.916 Sum_probs=29.9
Q ss_pred CCccchhcccCCCcceEEeecCCCCccccCCC
Q 029636 62 LPLDWERCLDLQSGRMYYFNRKSSKKSWSLPE 93 (190)
Q Consensus 62 LPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr 93 (190)
||.||+++.|.+ |++||+|+.|++++|++|+
T Consensus 1 lp~gW~~~~~~~-g~~yy~n~~t~~s~W~~P~ 31 (32)
T smart00456 1 LPPGWEERKDPD-GRPYYYNHETKETQWEKPR 31 (32)
T ss_pred CCCCCEEEECCC-CCEEEEECCCCCEEcCCCC
Confidence 799999999998 9999999999999999997
No 3
>cd00201 WW Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Probab=98.69 E-value=1.2e-08 Score=61.02 Aligned_cols=30 Identities=37% Similarity=0.936 Sum_probs=28.8
Q ss_pred CccchhcccCCCcceEEeecCCCCccccCCC
Q 029636 63 PLDWERCLDLQSGRMYYFNRKSSKKSWSLPE 93 (190)
Q Consensus 63 PsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr 93 (190)
|.+|+++.|.. |++||+|+.|++++|++|+
T Consensus 1 p~~W~~~~~~~-g~~yy~n~~t~~s~W~~P~ 30 (31)
T cd00201 1 PPGWEERWDPD-GRVYYYNHNTKETQWEDPR 30 (31)
T ss_pred CCCCEEEECCC-CCEEEEECCCCCEeCCCCC
Confidence 78999999998 9999999999999999997
No 4
>KOG3259 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=98.24 E-value=4.5e-07 Score=75.33 Aligned_cols=36 Identities=36% Similarity=0.880 Sum_probs=33.9
Q ss_pred CCCCCccchhcccCCCcceEEeecCCCCccccCCCc
Q 029636 59 KDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSLPEN 94 (190)
Q Consensus 59 ~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr~ 94 (190)
+..||.+||++.+..+|+.||||+.|++++|++|.+
T Consensus 4 ~~~LP~~Wekr~Srs~gr~YyfN~~T~~SqWe~P~~ 39 (163)
T KOG3259|consen 4 EEKLPPGWEKRMSRSSGRPYYFNTETNESQWERPSG 39 (163)
T ss_pred cccCCchhheeccccCCCcceeccccchhhccCCCc
Confidence 357999999999999999999999999999999995
No 5
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=97.31 E-value=0.00018 Score=63.70 Aligned_cols=64 Identities=25% Similarity=0.482 Sum_probs=52.0
Q ss_pred CCCCcccCC----------CCcCCceeeeccc---ccccCCCcccccccccCCCCCccchhcccCCCcceEEeecCCCCc
Q 029636 21 SNSSSESED----------NPSRKRKFLSDFS---LLKTEPAIQTSVDLQIKDPLPLDWERCLDLQSGRMYYFNRKSSKK 87 (190)
Q Consensus 21 ~~ssse~~~----------~~~~~R~~~~~~~---t~W~~P~~~~~iEL~l~~PLPsgWEq~LDlkSG~iYY~N~~T~~s 87 (190)
+|+-++|++ -...+||||.||. |-|..|-... -||.||++..|..-| +||+|..++.+
T Consensus 83 ~s~~~~sedlPLPpgWav~~T~~grkYYIDHn~~tTHW~HPlerE--------gLppGW~rv~s~e~G-tyY~~~~~k~t 153 (271)
T KOG1891|consen 83 RSSCDCSEDLPLPPGWAVEFTTEGRKYYIDHNNRTTHWVHPLERE--------GLPPGWKRVFSPEKG-TYYYHEEMKRT 153 (271)
T ss_pred cccCCCcccCCCCCCcceeeEecCceeEeecCCCcccccChhhhc--------cCCcchhhccccccc-eeeeecccchh
Confidence 355556664 3568999999887 8999994444 489999999998855 78899999999
Q ss_pred cccCCC
Q 029636 88 SWSLPE 93 (190)
Q Consensus 88 sw~dPr 93 (190)
++++|+
T Consensus 154 Qy~HPc 159 (271)
T KOG1891|consen 154 QYEHPC 159 (271)
T ss_pred hhcCCC
Confidence 999998
No 6
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=96.63 E-value=0.0022 Score=56.96 Aligned_cols=40 Identities=28% Similarity=0.646 Sum_probs=35.0
Q ss_pred cCCCCCccchhcccCCCcceEEeecCCCCccccCCCccccc
Q 029636 58 IKDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSLPENKQKL 98 (190)
Q Consensus 58 l~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr~~~~L 98 (190)
.++|||.||---.+.. |+.||++|++.++-|.+|-+..+|
T Consensus 90 edlPLPpgWav~~T~~-grkYYIDHn~~tTHW~HPlerEgL 129 (271)
T KOG1891|consen 90 EDLPLPPGWAVEFTTE-GRKYYIDHNNRTTHWVHPLEREGL 129 (271)
T ss_pred ccCCCCCCcceeeEec-CceeEeecCCCcccccChhhhccC
Confidence 3799999998877776 999999999999999999975554
No 7
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=96.34 E-value=0.0017 Score=62.27 Aligned_cols=61 Identities=16% Similarity=0.460 Sum_probs=42.5
Q ss_pred CcCCceeeeccc---ccccCCCccc-ccccccCCCCCccchhcccCCCcceEEeecCCCCccccCCCcc
Q 029636 31 PSRKRKFLSDFS---LLKTEPAIQT-SVDLQIKDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSLPENK 95 (190)
Q Consensus 31 ~~~~R~~~~~~~---t~W~~P~~~~-~iEL~l~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr~~ 95 (190)
.-.+|.||-|-. .+|+.|.... ..|+++. =.+|..|-+-. |++||+|.+|.++.|+-|.+.
T Consensus 22 ~~dgRiYYYN~~T~kS~weKPkell~~~e~~l~---~~~Wke~~Tad-GkvyyyN~~TREs~W~iP~e~ 86 (590)
T COG5104 22 APDGRIYYYNKRTGKSSWEKPKELLKGSEEDLD---VDPWKECRTAD-GKVYYYNSITRESRWKIPPER 86 (590)
T ss_pred CCCCceEEEecccccccccChHHHhcchHhhhc---hhhHHHHhhcC-CceEEecCccccccccCChhh
Confidence 345666665544 7899993222 2223332 12599999754 999999999999999999963
No 8
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=95.41 E-value=0.007 Score=58.23 Aligned_cols=30 Identities=37% Similarity=0.962 Sum_probs=27.1
Q ss_pred ccchhcccCCCcceEEeecCCCCccccCCCc
Q 029636 64 LDWERCLDLQSGRMYYFNRKSSKKSWSLPEN 94 (190)
Q Consensus 64 sgWEq~LDlkSG~iYY~N~~T~~ssw~dPr~ 94 (190)
++|+..-|.. |+|||+|..|++++|+.|.+
T Consensus 15 s~w~e~k~~d-gRiYYYN~~T~kS~weKPke 44 (590)
T COG5104 15 SEWEELKAPD-GRIYYYNKRTGKSSWEKPKE 44 (590)
T ss_pred HHHHHhhCCC-CceEEEecccccccccChHH
Confidence 4699998875 99999999999999999974
No 9
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=93.91 E-value=0.033 Score=56.32 Aligned_cols=34 Identities=32% Similarity=0.786 Sum_probs=31.4
Q ss_pred CCCCCccchhcccCCCcceEEeecCCCCccccCCC
Q 029636 59 KDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSLPE 93 (190)
Q Consensus 59 ~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr 93 (190)
.-|||..||....-+ |++||++++|..++|-|||
T Consensus 220 ~gplp~nwemayte~-gevyfiDhntkttswLdpr 253 (984)
T KOG3209|consen 220 LGPLPHNWEMAYTEQ-GEVYFIDHNTKTTSWLDPR 253 (984)
T ss_pred cCCCCccceEeEeec-CeeEeeecccccceecChh
Confidence 356999999999877 9999999999999999999
No 10
>KOG0940 consensus Ubiquitin protein ligase RSP5/NEDD4 [Posttranslational modification, protein turnover, chaperones]
Probab=90.35 E-value=0.19 Score=46.54 Aligned_cols=58 Identities=12% Similarity=0.076 Sum_probs=42.2
Q ss_pred ceeeecc----cccccCCCccccccccc--------CCCCCccchhcccCCCcceEEeecCCCCccccCCCcc
Q 029636 35 RKFLSDF----SLLKTEPAIQTSVDLQI--------KDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSLPENK 95 (190)
Q Consensus 35 R~~~~~~----~t~W~~P~~~~~iEL~l--------~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr~~ 95 (190)
+.||.+| +|+|.+|.+..+-+ |+ .+.|| +||++.|- +|+.||+|+.-++++|-+|++.
T Consensus 77 ~~~~~~~~~~~~tlq~~P~sg~~p~-~l~~~~~vg~~~~l~-~~h~~~~~-~g~r~F~~~i~~ktt~ldd~e~ 146 (358)
T KOG0940|consen 77 WYGLFQHSRKDYTLWLNPRSGVNPG-HLTYFRFVGGVLALA-GWHMRFTD-TGQRPFYKHILKKTTTLDDREA 146 (358)
T ss_pred ceeeeeecccccccccCCccCCCCC-ccccccccccccccc-ceeeEecC-CCceehhhhhhcCccccCchhh
Confidence 5555533 58999997663322 22 23444 79999986 4899999999999999999953
No 11
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=89.48 E-value=0.16 Score=36.61 Aligned_cols=25 Identities=32% Similarity=0.794 Sum_probs=19.7
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCccc
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFVH 162 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v 162 (190)
|..-+|.+|+..+ ....||+|.+.-
T Consensus 1 M~~kAC~~C~~i~----~~~~CP~Cgs~~ 25 (61)
T PRK08351 1 MTEKACRHCHYIT----TEDRCPVCGSRD 25 (61)
T ss_pred CchhhhhhCCccc----CCCcCCCCcCCc
Confidence 4456999999877 455899999965
No 12
>cd00201 WW Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Probab=87.87 E-value=0.4 Score=28.07 Aligned_cols=16 Identities=13% Similarity=0.237 Sum_probs=13.3
Q ss_pred Cceeeeccc---ccccCCC
Q 029636 34 KRKFLSDFS---LLKTEPA 49 (190)
Q Consensus 34 ~R~~~~~~~---t~W~~P~ 49 (190)
+|.||.|+. ++|+.|.
T Consensus 12 g~~yy~n~~t~~s~W~~P~ 30 (31)
T cd00201 12 GRVYYYNHNTKETQWEDPR 30 (31)
T ss_pred CCEEEEECCCCCEeCCCCC
Confidence 788888766 9999984
No 13
>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....
Probab=86.76 E-value=0.41 Score=29.19 Aligned_cols=16 Identities=13% Similarity=0.189 Sum_probs=14.0
Q ss_pred CCceeeeccc---ccccCC
Q 029636 33 RKRKFLSDFS---LLKTEP 48 (190)
Q Consensus 33 ~~R~~~~~~~---t~W~~P 48 (190)
.+|.||.|+. ++|++|
T Consensus 13 ~g~~YY~N~~t~~s~W~~P 31 (31)
T PF00397_consen 13 SGRPYYYNHETGESQWERP 31 (31)
T ss_dssp TSEEEEEETTTTEEESSST
T ss_pred CCCEEEEeCCCCCEEeCCC
Confidence 6899999887 899987
No 14
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=83.60 E-value=0.65 Score=34.13 Aligned_cols=25 Identities=28% Similarity=0.600 Sum_probs=18.9
Q ss_pred cCCCCCccchhcccC-------CCcceEEeec
Q 029636 58 IKDPLPLDWERCLDL-------QSGRMYYFNR 82 (190)
Q Consensus 58 l~~PLPsgWEq~LDl-------kSG~iYY~N~ 82 (190)
++.|||.||+..+-+ ..+.|||+..
T Consensus 4 ~~~Plp~GW~R~~~~r~~g~~~~~~dV~Y~sP 35 (77)
T smart00391 4 LRLPLPCGWRRETKQRKSGRSAGKFDVYYISP 35 (77)
T ss_pred ccCCCCCCcEEEEEEecCCCCCCcccEEEECC
Confidence 467899999987752 2378999964
No 15
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=83.01 E-value=1 Score=31.33 Aligned_cols=26 Identities=38% Similarity=0.936 Sum_probs=20.0
Q ss_pred cCCCCCccchhcccC------CCcceEEeecC
Q 029636 58 IKDPLPLDWERCLDL------QSGRMYYFNRK 83 (190)
Q Consensus 58 l~~PLPsgWEq~LDl------kSG~iYY~N~~ 83 (190)
+..|||.||+..+-+ ..+.|||+...
T Consensus 2 l~~P~p~GW~R~~~~r~~g~~~k~dv~Y~sP~ 33 (62)
T cd00122 2 LRDPLPPGWKRELVIRKSGSAGKGDVYYYSPC 33 (62)
T ss_pred CCCCCCCCeEEEEEEcCCCCCCcceEEEECCC
Confidence 568999999998764 23678999765
No 16
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=82.74 E-value=0.46 Score=34.58 Aligned_cols=24 Identities=25% Similarity=0.438 Sum_probs=19.6
Q ss_pred EEeeCccceeeeeecCCCCCCCCCCccc
Q 029636 135 VALACMNCHLLVILSKSSPSCPNCKFVH 162 (190)
Q Consensus 135 v~~gC~~Clmyvm~~k~~p~CP~Ck~~v 162 (190)
...+|.+|+..+ .+..||.|.+.-
T Consensus 4 ~~~AC~~C~~i~----~~~~Cp~Cgs~~ 27 (64)
T PRK06393 4 QYRACKKCKRLT----PEKTCPVHGDEK 27 (64)
T ss_pred hhhhHhhCCccc----CCCcCCCCCCCc
Confidence 456899999888 566999999964
No 17
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=80.37 E-value=1.2 Score=45.55 Aligned_cols=62 Identities=18% Similarity=0.337 Sum_probs=43.4
Q ss_pred CcCCceeeeccc---ccccCCCcccccccc---cCCCCCccchhcccCCCcceEEeecCCCCccccCCC
Q 029636 31 PSRKRKFLSDFS---LLKTEPAIQTSVDLQ---IKDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSLPE 93 (190)
Q Consensus 31 ~~~~R~~~~~~~---t~W~~P~~~~~iEL~---l~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr 93 (190)
...+-.||-||. |+|=+|+-.-...-+ -+.-||.|||+--|+. =.+||+.|....+.++.|-
T Consensus 232 te~gevyfiDhntkttswLdprl~kkaK~~eeckd~elPygWeki~dpi-Yg~yyvdHiN~~sq~enpv 299 (984)
T KOG3209|consen 232 TEQGEVYFIDHNTKTTSWLDPRLTKKAKPPEECKDQELPYGWEKIEDPI-YGTYYVDHINRKSQYENPV 299 (984)
T ss_pred eecCeeEeeecccccceecChhhhcccCChhhcccccccccccccCCcc-ceeEEecccchhhhhccch
Confidence 445668889998 899999632222111 2345999999999998 4567788887777666665
No 18
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.56 E-value=1.9 Score=28.19 Aligned_cols=34 Identities=24% Similarity=0.528 Sum_probs=26.4
Q ss_pred eEEeeCccceeeeeecCC--CCCCCCCCcccCCCCC
Q 029636 134 MVALACMNCHLLVILSKS--SPSCPNCKFVHSLPNQ 167 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~--~p~CP~Ck~~v~~~~~ 167 (190)
|+..-|++|.--+-+... ..+||+|.+.+.....
T Consensus 1 ~~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 1 MAEYKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred CCEEECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 677889999988776664 5899999987765443
No 19
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=69.39 E-value=3 Score=25.96 Aligned_cols=26 Identities=27% Similarity=0.604 Sum_probs=19.6
Q ss_pred eeCccceeeeeecCC-------CCCCCCCCccc
Q 029636 137 LACMNCHLLVILSKS-------SPSCPNCKFVH 162 (190)
Q Consensus 137 ~gC~~Clmyvm~~k~-------~p~CP~Ck~~v 162 (190)
+-||+|.--+.|... ..+||+|+...
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 579999988888742 25899998753
No 20
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=66.90 E-value=2.4 Score=33.22 Aligned_cols=32 Identities=22% Similarity=0.371 Sum_probs=22.3
Q ss_pred CCeEEeeCccceeeeeecCCC--CCCCCCCcccC
Q 029636 132 NNMVALACMNCHLLVILSKSS--PSCPNCKFVHS 163 (190)
Q Consensus 132 ~~mv~~gC~~Clmyvm~~k~~--p~CP~Ck~~v~ 163 (190)
=-|+-+.|..|-.-+-=-+-+ -+||+|||--.
T Consensus 54 Llv~Pa~CkkCGfef~~~~ik~pSRCP~CKSE~I 87 (97)
T COG3357 54 LLVRPARCKKCGFEFRDDKIKKPSRCPKCKSEWI 87 (97)
T ss_pred EEecChhhcccCccccccccCCcccCCcchhhcc
Confidence 347778999998655432333 49999998643
No 21
>cd01397 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.
Probab=66.36 E-value=4 Score=30.27 Aligned_cols=24 Identities=29% Similarity=0.731 Sum_probs=18.0
Q ss_pred cCCCCCccchhcccC------CCcceEEee
Q 029636 58 IKDPLPLDWERCLDL------QSGRMYYFN 81 (190)
Q Consensus 58 l~~PLPsgWEq~LDl------kSG~iYY~N 81 (190)
+-.|||.||+.-+=+ .-|.|||+-
T Consensus 2 ~r~Pl~~GW~Re~vir~~~~~~~~dV~Y~a 31 (73)
T cd01397 2 LRVPLELGWRRETRIRGLGGRIQGEVAYYA 31 (73)
T ss_pred ccCCCCCCceeEEEeccCCCCccceEEEEC
Confidence 457999999986643 347899984
No 22
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=65.97 E-value=5 Score=31.45 Aligned_cols=27 Identities=30% Similarity=0.688 Sum_probs=22.0
Q ss_pred eCccceeeee-ecCCCC-CCCCCCcccCCC
Q 029636 138 ACMNCHLLVI-LSKSSP-SCPNCKFVHSLP 165 (190)
Q Consensus 138 gC~~Clmyvm-~~k~~p-~CP~Ck~~v~~~ 165 (190)
.|+.|---+- |.| +| .||+|...+++.
T Consensus 11 ~Cp~CG~kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCCC-CCccCCCCCCccCcc
Confidence 5999987665 677 55 599999999988
No 23
>KOG0940 consensus Ubiquitin protein ligase RSP5/NEDD4 [Posttranslational modification, protein turnover, chaperones]
Probab=65.43 E-value=5.5 Score=37.04 Aligned_cols=47 Identities=15% Similarity=0.162 Sum_probs=36.8
Q ss_pred CCccccccccc-CCCCCccchhcccCCCc--ceEEeecCCC-CccccCCCc
Q 029636 48 PAIQTSVDLQI-KDPLPLDWERCLDLQSG--RMYYFNRKSS-KKSWSLPEN 94 (190)
Q Consensus 48 P~~~~~iEL~l-~~PLPsgWEq~LDlkSG--~iYY~N~~T~-~ssw~dPr~ 94 (190)
+...+..|..+ ..+||.+|+..++..-| ..||+|+.+. .++|.+|.-
T Consensus 46 l~~~~~~ee~ldy~glprewf~~lS~e~~~p~~~~~~~~~~~~tlq~~P~s 96 (358)
T KOG0940|consen 46 LMREFKGEEGLDYGGLPREWFFLLSHEGFNPWYGLFQHSRKDYTLWLNPRS 96 (358)
T ss_pred ceeecccccccccCCCCcceeeeeccccCCcceeeeeecccccccccCCcc
Confidence 34455556554 47899999999998844 9999999998 599999983
No 24
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
Probab=64.33 E-value=3.7 Score=29.66 Aligned_cols=29 Identities=31% Similarity=0.721 Sum_probs=18.8
Q ss_pred cCCCCCccchhccc-CCC------cceEEeecCCCCc
Q 029636 58 IKDPLPLDWERCLD-LQS------GRMYYFNRKSSKK 87 (190)
Q Consensus 58 l~~PLPsgWEq~LD-lkS------G~iYY~N~~T~~s 87 (190)
+..|||.||+.-+= .++ +.+||+.. +|++
T Consensus 7 ~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP-~Gk~ 42 (77)
T PF01429_consen 7 LDPPLPDGWKREVVVRKSGSSAGKKDVYYYSP-CGKR 42 (77)
T ss_dssp EBTTSTTT-EEEEEESSSSTTTTSEEEEEEET-TSEE
T ss_pred ccCCCCCCCEEEEEEecCCCcCCceEEEEECC-CCCE
Confidence 46899999987554 222 47799986 5544
No 25
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=60.52 E-value=7 Score=30.38 Aligned_cols=29 Identities=24% Similarity=0.438 Sum_probs=23.4
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCccc
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFVH 162 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v 162 (190)
-+.+-|..|--++=+....-.||+|++..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 46789999997777766677899999853
No 26
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=58.33 E-value=9.6 Score=31.31 Aligned_cols=36 Identities=31% Similarity=0.571 Sum_probs=26.1
Q ss_pred CCCCCCCeEEeeCccceeeeeecCCC--CCCCCCCccc
Q 029636 127 LSSASNNMVALACMNCHLLVILSKSS--PSCPNCKFVH 162 (190)
Q Consensus 127 ~s~~~~~mv~~gC~~Clmyvm~~k~~--p~CP~Ck~~v 162 (190)
.+|+..++=.-.|.+|.--+-+.... |.||+|....
T Consensus 103 ~sGE~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 103 HSGEVVGPGTLVCENCGHEVELTHPERLPPCPKCGHTE 140 (146)
T ss_pred ecCcEecCceEecccCCCEEEecCCCcCCCCCCCCCCe
Confidence 34555566667799998777776644 9999998753
No 27
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=58.17 E-value=8 Score=30.09 Aligned_cols=29 Identities=24% Similarity=0.464 Sum_probs=22.8
Q ss_pred eEEeeCccceeeeeecCCC-CCCCCCCccc
Q 029636 134 MVALACMNCHLLVILSKSS-PSCPNCKFVH 162 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~-p~CP~Ck~~v 162 (190)
-+.+-|..|--++=+.... -.||+|++..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence 4678899999887776554 6799999764
No 28
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=57.86 E-value=8.6 Score=29.86 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=22.5
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCcc
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFV 161 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~ 161 (190)
-+.+-|..|--.+=+....-.||+|++.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 4678899999777776666679999975
No 29
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=57.26 E-value=5.5 Score=37.19 Aligned_cols=27 Identities=30% Similarity=0.737 Sum_probs=20.0
Q ss_pred EeeCccceeeeeecCCCCCCCCCCcccC
Q 029636 136 ALACMNCHLLVILSKSSPSCPNCKFVHS 163 (190)
Q Consensus 136 ~~gC~~Clmyvm~~k~~p~CP~Ck~~v~ 163 (190)
+.+|+.|...+ -..+..+||||+...-
T Consensus 215 ~~~C~~Cd~~~-~~~~~a~CpRC~~~L~ 241 (403)
T TIGR00155 215 LRSCSACHTTI-LPAQEPVCPRCSTPLY 241 (403)
T ss_pred CCcCCCCCCcc-CCCCCcCCcCCCCccc
Confidence 55799999844 2345578999998763
No 30
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=56.92 E-value=7.5 Score=24.22 Aligned_cols=28 Identities=21% Similarity=0.681 Sum_probs=17.8
Q ss_pred CCeEEeeCccceeeeeecCCCCCCCCCCcc
Q 029636 132 NNMVALACMNCHLLVILSKSSPSCPNCKFV 161 (190)
Q Consensus 132 ~~mv~~gC~~Clmyvm~~k~~p~CP~Ck~~ 161 (190)
..+++.-|..|--++.-++ +.||+|.+.
T Consensus 7 ~~l~~~rC~~Cg~~~~pPr--~~Cp~C~s~ 34 (37)
T PF12172_consen 7 GRLLGQRCRDCGRVQFPPR--PVCPHCGSD 34 (37)
T ss_dssp T-EEEEE-TTT--EEES----SEETTTT--
T ss_pred CEEEEEEcCCCCCEecCCC--cCCCCcCcc
Confidence 5588999999999988877 899999753
No 31
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=56.69 E-value=4.1 Score=34.61 Aligned_cols=30 Identities=23% Similarity=0.463 Sum_probs=23.5
Q ss_pred EEeeCccceeeeeecC---CCCCCCCCCcccCC
Q 029636 135 VALACMNCHLLVILSK---SSPSCPNCKFVHSL 164 (190)
Q Consensus 135 v~~gC~~Clmyvm~~k---~~p~CP~Ck~~v~~ 164 (190)
.--.|+.|++++=+-+ ..-.||+|++.+--
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred CceeCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence 3456899999997765 45899999998753
No 32
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=56.33 E-value=4.4 Score=25.75 Aligned_cols=25 Identities=28% Similarity=0.774 Sum_probs=16.7
Q ss_pred eeCccceeeeeecCC-------CCCCCCCCcc
Q 029636 137 LACMNCHLLVILSKS-------SPSCPNCKFV 161 (190)
Q Consensus 137 ~gC~~Clmyvm~~k~-------~p~CP~Ck~~ 161 (190)
.-||+|.--+-|..+ .-+||+|+.+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 458888777766653 3478888754
No 33
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=55.73 E-value=15 Score=26.00 Aligned_cols=29 Identities=21% Similarity=0.496 Sum_probs=23.2
Q ss_pred EEeeCccceeeeeecCCCCCCCCCCcccCCCCC
Q 029636 135 VALACMNCHLLVILSKSSPSCPNCKFVHSLPNQ 167 (190)
Q Consensus 135 v~~gC~~Clmyvm~~k~~p~CP~Ck~~v~~~~~ 167 (190)
-.--|+.|-.|-| ...||.|......+++
T Consensus 4 ~mr~C~~CgvYTL----k~~CP~CG~~t~~~~P 32 (56)
T PRK13130 4 KIRKCPKCGVYTL----KEICPVCGGKTKNPHP 32 (56)
T ss_pred cceECCCCCCEEc----cccCcCCCCCCCCCCC
Confidence 4567999999999 6789999987665554
No 34
>KOG0155 consensus Transcription factor CA150 [Transcription]
Probab=54.78 E-value=9 Score=38.06 Aligned_cols=35 Identities=29% Similarity=0.723 Sum_probs=27.1
Q ss_pred CCCCCc-cchhcccCCCcceEEeecCCCCccccCCCc
Q 029636 59 KDPLPL-DWERCLDLQSGRMYYFNRKSSKKSWSLPEN 94 (190)
Q Consensus 59 ~~PLPs-gWEq~LDlkSG~iYY~N~~T~~ssw~dPr~ 94 (190)
..|+|- +|=---+ ..|++||+|..|..+.|+.|.+
T Consensus 108 ~~~ipgtdWcVVwT-gD~RvFFyNpktk~S~We~P~d 143 (617)
T KOG0155|consen 108 KKPIPGTDWCVVWT-GDNRVFFYNPKTKLSVWERPLD 143 (617)
T ss_pred CCCCCCCCeEEEEe-CCCceEEeCCccccccccCchh
Confidence 455776 4843333 4489999999999999999995
No 35
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=53.21 E-value=15 Score=26.50 Aligned_cols=28 Identities=21% Similarity=0.526 Sum_probs=22.2
Q ss_pred EeeCccceeeeeecCCCCCCCCCCcccCCCCC
Q 029636 136 ALACMNCHLLVILSKSSPSCPNCKFVHSLPNQ 167 (190)
Q Consensus 136 ~~gC~~Clmyvm~~k~~p~CP~Ck~~v~~~~~ 167 (190)
.--|+.|.-|-|= .+||.|....-.+++
T Consensus 5 ~rkC~~cg~YTLk----e~Cp~CG~~t~~~~P 32 (59)
T COG2260 5 IRKCPKCGRYTLK----EKCPVCGGDTKVPHP 32 (59)
T ss_pred hhcCcCCCceeec----ccCCCCCCccccCCC
Confidence 4569999999874 789999988766554
No 36
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=51.75 E-value=7.7 Score=36.48 Aligned_cols=26 Identities=23% Similarity=0.669 Sum_probs=20.0
Q ss_pred EeeCccceeeeeecCCCCCCCCCCcccC
Q 029636 136 ALACMNCHLLVILSKSSPSCPNCKFVHS 163 (190)
Q Consensus 136 ~~gC~~Clmyvm~~k~~p~CP~Ck~~v~ 163 (190)
+.+|+.|...+ ..+.-+||||+...-
T Consensus 221 l~~C~~Cd~l~--~~~~a~CpRC~~~L~ 246 (419)
T PRK15103 221 LRSCSCCTAIL--PADQPVCPRCHTKGY 246 (419)
T ss_pred CCcCCCCCCCC--CCCCCCCCCCCCcCc
Confidence 55799999853 445568999998873
No 37
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=50.92 E-value=5.8 Score=30.64 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=21.9
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCccc
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFVH 162 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v 162 (190)
-+.+-|..|-..+-+....-.||+|++..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp --EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred CCcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 46789999999999888888899999863
No 38
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=50.74 E-value=8.6 Score=30.96 Aligned_cols=34 Identities=26% Similarity=0.527 Sum_probs=28.1
Q ss_pred eEEeeCccceeee-eecCCCCCCCCCCcccCCCCCC
Q 029636 134 MVALACMNCHLLV-ILSKSSPSCPNCKFVHSLPNQQ 168 (190)
Q Consensus 134 mv~~gC~~Clmyv-m~~k~~p~CP~Ck~~v~~~~~~ 168 (190)
-|.+-||.|.=.- |+-+.| .|+.|+...-+|+..
T Consensus 67 av~V~CP~C~K~TKmLGr~D-~CM~C~~pLTLd~~l 101 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRVD-ACMHCKEPLTLDPSL 101 (114)
T ss_pred ceeeECCCCCChHhhhchhh-ccCcCCCcCccCchh
Confidence 3777899999877 677776 999999999888763
No 39
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=50.61 E-value=11 Score=24.43 Aligned_cols=28 Identities=18% Similarity=0.546 Sum_probs=18.5
Q ss_pred eCccceeeeeecCC----CCCCCCCCcccCCC
Q 029636 138 ACMNCHLLVILSKS----SPSCPNCKFVHSLP 165 (190)
Q Consensus 138 gC~~Clmyvm~~k~----~p~CP~Ck~~v~~~ 165 (190)
-||.|.-.+...+. .-.||.|.+.....
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECC
Confidence 38888764444432 35699999887664
No 40
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=50.38 E-value=9.5 Score=32.99 Aligned_cols=33 Identities=18% Similarity=0.476 Sum_probs=25.1
Q ss_pred CCCCeEEeeCccceeeeeecCCCCCCCCCCccc
Q 029636 130 ASNNMVALACMNCHLLVILSKSSPSCPNCKFVH 162 (190)
Q Consensus 130 ~~~~mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v 162 (190)
..-+.|-|-|.+|---.+.-...-+||+|..+.
T Consensus 143 ~dlGVI~A~CsrC~~~L~~~~~~l~Cp~Cg~tE 175 (188)
T COG1096 143 NDLGVIYARCSRCRAPLVKKGNMLKCPNCGNTE 175 (188)
T ss_pred CcceEEEEEccCCCcceEEcCcEEECCCCCCEE
Confidence 445689999999986655544558999998754
No 41
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=50.25 E-value=8.1 Score=28.68 Aligned_cols=11 Identities=36% Similarity=1.238 Sum_probs=8.8
Q ss_pred cCCCCCCCCCC
Q 029636 149 SKSSPSCPNCK 159 (190)
Q Consensus 149 ~k~~p~CP~Ck 159 (190)
-..+|+||+|+
T Consensus 81 ~~~np~C~~C~ 91 (91)
T cd04482 81 ERENPVCPKCG 91 (91)
T ss_pred EEcCCcCCCCC
Confidence 34789999995
No 42
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=47.72 E-value=7.8 Score=27.21 Aligned_cols=31 Identities=23% Similarity=0.639 Sum_probs=20.9
Q ss_pred eeCccceeeeeec----CCCCCCCCCCcccCCCCC
Q 029636 137 LACMNCHLLVILS----KSSPSCPNCKFVHSLPNQ 167 (190)
Q Consensus 137 ~gC~~Clmyvm~~----k~~p~CP~Ck~~v~~~~~ 167 (190)
.-|.+|.=..+-. .-.-|||||+.+..+...
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~ 39 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRAT 39 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCccceEecc
Confidence 4577776544433 235799999999876554
No 43
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=47.15 E-value=11 Score=22.73 Aligned_cols=20 Identities=35% Similarity=0.946 Sum_probs=11.0
Q ss_pred CccceeeeeecCCCCCCCCCCc
Q 029636 139 CMNCHLLVILSKSSPSCPNCKF 160 (190)
Q Consensus 139 C~~Clmyvm~~k~~p~CP~Ck~ 160 (190)
||.|-.-| +.+.-.||.|..
T Consensus 3 CP~C~~~V--~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 3 CPECGAEV--PESAKFCPHCGY 22 (26)
T ss_pred CCCCcCCc--hhhcCcCCCCCC
Confidence 55665443 445556666654
No 44
>KOG3259 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=46.73 E-value=11 Score=31.84 Aligned_cols=23 Identities=13% Similarity=0.082 Sum_probs=17.8
Q ss_pred CcCCceeeeccc---ccccCCCcccc
Q 029636 31 PSRKRKFLSDFS---LLKTEPAIQTS 53 (190)
Q Consensus 31 ~~~~R~~~~~~~---t~W~~P~~~~~ 53 (190)
..++|.||-|+. .||++|.....
T Consensus 17 rs~gr~YyfN~~T~~SqWe~P~~t~~ 42 (163)
T KOG3259|consen 17 RSSGRPYYFNTETNESQWERPSGTSK 42 (163)
T ss_pred ccCCCcceeccccchhhccCCCcccc
Confidence 467899998887 79999965543
No 45
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=45.31 E-value=17 Score=29.89 Aligned_cols=29 Identities=14% Similarity=0.119 Sum_probs=23.5
Q ss_pred eCccceeeee-ecCCCCCCCCCCcccCCCC
Q 029636 138 ACMNCHLLVI-LSKSSPSCPNCKFVHSLPN 166 (190)
Q Consensus 138 gC~~Clmyvm-~~k~~p~CP~Ck~~v~~~~ 166 (190)
.||.|---+- |.|.-..||+|...+++..
T Consensus 11 ~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 11 ICPNTGSKFYDLNRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred cCCCcCccccccCCCCccCCCcCCccCcch
Confidence 5999976554 7787789999999998763
No 46
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.01 E-value=21 Score=28.48 Aligned_cols=29 Identities=28% Similarity=0.484 Sum_probs=21.2
Q ss_pred eEEeeCccceeeeeec---------------------CCCCCCCCCCccc
Q 029636 134 MVALACMNCHLLVILS---------------------KSSPSCPNCKFVH 162 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~---------------------k~~p~CP~Ck~~v 162 (190)
-+.+-|+.|--.+-+. ...-+||+|++..
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 4778899998665554 3456799999863
No 47
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=43.96 E-value=18 Score=28.41 Aligned_cols=17 Identities=24% Similarity=0.483 Sum_probs=13.6
Q ss_pred CCCeEEeeCccceeeee
Q 029636 131 SNNMVALACMNCHLLVI 147 (190)
Q Consensus 131 ~~~mv~~gC~~Clmyvm 147 (190)
....|+.||++|..-++
T Consensus 44 ~~vvvvggCp~CrvG~l 60 (98)
T PF10164_consen 44 PQVVVVGGCPACRVGVL 60 (98)
T ss_pred CceEEecCCCCCceeee
Confidence 34688999999987665
No 48
>PRK00420 hypothetical protein; Validated
Probab=42.93 E-value=12 Score=29.84 Aligned_cols=35 Identities=20% Similarity=0.326 Sum_probs=26.9
Q ss_pred CCCeEEeeCccceeeeee-cCCCCCCCCCCcccCCC
Q 029636 131 SNNMVALACMNCHLLVIL-SKSSPSCPNCKFVHSLP 165 (190)
Q Consensus 131 ~~~mv~~gC~~Clmyvm~-~k~~p~CP~Ck~~v~~~ 165 (190)
+..|....||.|-.-.+= ....-.||+|...+-..
T Consensus 18 Ga~ml~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 18 GAKMLSKHCPVCGLPLFELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred HHHHccCCCCCCCCcceecCCCceECCCCCCeeeec
Confidence 456888999999965553 56778999999976543
No 49
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=42.40 E-value=10 Score=27.33 Aligned_cols=11 Identities=45% Similarity=1.044 Sum_probs=9.0
Q ss_pred CCCCCCCcccC
Q 029636 153 PSCPNCKFVHS 163 (190)
Q Consensus 153 p~CP~Ck~~v~ 163 (190)
-||||||-+.-
T Consensus 25 ~KCPrCK~vN~ 35 (60)
T COG4416 25 KKCPRCKEVNE 35 (60)
T ss_pred ecCCccceeee
Confidence 69999998763
No 50
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.94 E-value=15 Score=28.63 Aligned_cols=29 Identities=21% Similarity=0.487 Sum_probs=21.8
Q ss_pred eEEeeCccceeeeeecC-CCCCCCCCCccc
Q 029636 134 MVALACMNCHLLVILSK-SSPSCPNCKFVH 162 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k-~~p~CP~Ck~~v 162 (190)
-+.+-|..|--++=+.. ...+||+|++..
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence 46788999997766654 345799999853
No 51
>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only]
Probab=41.87 E-value=17 Score=36.21 Aligned_cols=39 Identities=31% Similarity=0.489 Sum_probs=32.9
Q ss_pred cccccCCCCCccchhcccCCCcceEEeecCCCCccccCCC
Q 029636 54 VDLQIKDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSLPE 93 (190)
Q Consensus 54 iEL~l~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr 93 (190)
+.|+.--|||.||-+-. -+||-..|+...|+.-+|.+|-
T Consensus 147 ~~l~~~epLPeGW~~i~-HnSGmPvylHr~tRVvt~SrPY 185 (650)
T KOG4334|consen 147 IDLDKSEPLPEGWTVIS-HNSGMPVYLHRFTRVVTHSRPY 185 (650)
T ss_pred ccCCCCCcCCCceEEEe-ecCCCceEEeeeeeeEeccCce
Confidence 34666789999998765 4789999999999999999987
No 52
>PRK11032 hypothetical protein; Provisional
Probab=41.85 E-value=24 Score=29.64 Aligned_cols=35 Identities=26% Similarity=0.564 Sum_probs=24.2
Q ss_pred CCCCCCeEEeeCccceeeeeecC--CCCCCCCCCccc
Q 029636 128 SSASNNMVALACMNCHLLVILSK--SSPSCPNCKFVH 162 (190)
Q Consensus 128 s~~~~~mv~~gC~~Clmyvm~~k--~~p~CP~Ck~~v 162 (190)
+|+-.++=...|.+|.--+-+.+ .-|.||+|....
T Consensus 116 sGEvvg~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~ 152 (160)
T PRK11032 116 SGEVVGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQ 152 (160)
T ss_pred cceeeecceEEecCCCCEEEecCCCcCCCCCCCCCCe
Confidence 34545555567999976665555 459999998764
No 53
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=41.33 E-value=19 Score=22.16 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=15.1
Q ss_pred eCccceeeeeecCCCCCCCCCCc
Q 029636 138 ACMNCHLLVILSKSSPSCPNCKF 160 (190)
Q Consensus 138 gC~~Clmyvm~~k~~p~CP~Ck~ 160 (190)
.|..|-.-+--.+.+.+||.|+.
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCC
Confidence 47777644333446679999975
No 54
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=40.91 E-value=14 Score=23.33 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=16.6
Q ss_pred eCccceeeeeecCCC-CCCCCCCccc
Q 029636 138 ACMNCHLLVILSKSS-PSCPNCKFVH 162 (190)
Q Consensus 138 gC~~Clmyvm~~k~~-p~CP~Ck~~v 162 (190)
-|..|-.-|-+...+ -+||.|..-+
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCeE
Confidence 377888888766655 4899887654
No 55
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=40.46 E-value=14 Score=30.14 Aligned_cols=28 Identities=18% Similarity=0.454 Sum_probs=20.5
Q ss_pred EEeeCccceeeeeec---CCCCCCCCCCccc
Q 029636 135 VALACMNCHLLVILS---KSSPSCPNCKFVH 162 (190)
Q Consensus 135 v~~gC~~Clmyvm~~---k~~p~CP~Ck~~v 162 (190)
.--.||+|..-+-.- ..+-.||+|..+.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 345799998766433 3579999999875
No 56
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=40.44 E-value=11 Score=23.52 Aligned_cols=12 Identities=33% Similarity=0.742 Sum_probs=3.4
Q ss_pred CCCCCCCCcccC
Q 029636 152 SPSCPNCKFVHS 163 (190)
Q Consensus 152 ~p~CP~Ck~~v~ 163 (190)
-|+||+|.+..-
T Consensus 2 ~p~Cp~C~se~~ 13 (30)
T PF08274_consen 2 LPKCPLCGSEYT 13 (30)
T ss_dssp S---TTT-----
T ss_pred CCCCCCCCCcce
Confidence 489999998653
No 57
>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]
Probab=39.75 E-value=9.7 Score=40.38 Aligned_cols=32 Identities=31% Similarity=0.748 Sum_probs=24.8
Q ss_pred CCCCCccchhcccCCCcceEEeecCCCCccccC
Q 029636 59 KDPLPLDWERCLDLQSGRMYYFNRKSSKKSWSL 91 (190)
Q Consensus 59 ~~PLPsgWEq~LDlkSG~iYY~N~~T~~ssw~d 91 (190)
+-.||.+|+...|-+ |+-||+|+-...+++++
T Consensus 17 ~~~v~~~~~r~~dsk-~r~~y~~~~~~~~~~~~ 48 (1298)
T KOG3552|consen 17 HEELSYGWERAIDSK-GRSYYINHLNKTTTYEA 48 (1298)
T ss_pred ccccchHHHHhhhcc-cchhHHhhcCCccCcCC
Confidence 356899999999987 88888887776665444
No 58
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=37.77 E-value=12 Score=38.88 Aligned_cols=28 Identities=29% Similarity=0.768 Sum_probs=24.6
Q ss_pred cchhcccCCCcceEEeecCCCCccccCCC
Q 029636 65 DWERCLDLQSGRMYYFNRKSSKKSWSLPE 93 (190)
Q Consensus 65 gWEq~LDlkSG~iYY~N~~T~~ssw~dPr 93 (190)
-||..... .--.||+|+.|.++.|++|-
T Consensus 353 pw~rais~-nkvpyyinh~~q~t~wdhp~ 380 (966)
T KOG4286|consen 353 PWERAISP-NKVPYYINHETQTTCWDHPK 380 (966)
T ss_pred cchhccCc-cccchhhcccchhhhccchH
Confidence 39999887 36669999999999999998
No 59
>PF14369 zf-RING_3: zinc-finger
Probab=37.08 E-value=31 Score=21.91 Aligned_cols=22 Identities=32% Similarity=0.865 Sum_probs=14.6
Q ss_pred Cccceeeeeec--CCCC-CCCCCCc
Q 029636 139 CMNCHLLVILS--KSSP-SCPNCKF 160 (190)
Q Consensus 139 C~~Clmyvm~~--k~~p-~CP~Ck~ 160 (190)
|=.|-..|=+. ..+. .||+|.+
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcCCCC
Confidence 66777777664 2334 4999975
No 60
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=37.02 E-value=18 Score=34.26 Aligned_cols=31 Identities=19% Similarity=0.466 Sum_probs=25.7
Q ss_pred eEEeeCccc-eeeeeecCCCCCCCCCCcccCC
Q 029636 134 MVALACMNC-HLLVILSKSSPSCPNCKFVHSL 164 (190)
Q Consensus 134 mv~~gC~~C-lmyvm~~k~~p~CP~Ck~~v~~ 164 (190)
.-..-|++| ..+-+....+.+||+|...+..
T Consensus 238 g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~ 269 (380)
T COG1867 238 GYIYHCSRCGEIVGSFREVDEKCPHCGGKVHL 269 (380)
T ss_pred CcEEEcccccceecccccccccCCccccccee
Confidence 456889999 5888889999999999986643
No 61
>KOG0155 consensus Transcription factor CA150 [Transcription]
Probab=36.92 E-value=20 Score=35.73 Aligned_cols=31 Identities=26% Similarity=0.651 Sum_probs=27.1
Q ss_pred CccchhcccCCCcceEEeecCCCCccccCCCc
Q 029636 63 PLDWERCLDLQSGRMYYFNRKSSKKSWSLPEN 94 (190)
Q Consensus 63 PsgWEq~LDlkSG~iYY~N~~T~~ssw~dPr~ 94 (190)
|++|-.+--+. |..||+|-.|.+.+|++|..
T Consensus 11 ps~wtef~ap~-G~pyy~ns~t~~st~ekP~~ 41 (617)
T KOG0155|consen 11 PSGWTEFKAPD-GIPYYWNSETLESTWEKPSF 41 (617)
T ss_pred CCCCccCCCCC-CcceecccccccchhhCchh
Confidence 48898887664 99999999999999999993
No 62
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=36.75 E-value=11 Score=27.55 Aligned_cols=26 Identities=31% Similarity=0.657 Sum_probs=19.2
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCcc
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFV 161 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~ 161 (190)
|.--+|.+|+-. +.....-||.|.+.
T Consensus 2 ~~~kAC~~Ck~l--~~~d~e~CP~Cgs~ 27 (64)
T COG2093 2 STEKACKNCKRL--TPEDTEICPVCGST 27 (64)
T ss_pred chhHHHhhcccc--CCCCCccCCCCCCc
Confidence 344579999853 46666779999987
No 63
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=36.53 E-value=19 Score=29.79 Aligned_cols=17 Identities=35% Similarity=0.817 Sum_probs=14.9
Q ss_pred cchhcccCCCcceEEee
Q 029636 65 DWERCLDLQSGRMYYFN 81 (190)
Q Consensus 65 gWEq~LDlkSG~iYY~N 81 (190)
+++-+||++||+|+|+.
T Consensus 21 e~~~yLD~~TGeI~~~~ 37 (163)
T PF03682_consen 21 EREYYLDLETGEIFYVS 37 (163)
T ss_pred cceEEEECCCCeEEEee
Confidence 57889999999999984
No 64
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=35.60 E-value=22 Score=29.80 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=21.3
Q ss_pred EEeeCccceeeeeec---CCCCCCCCCCcccCC
Q 029636 135 VALACMNCHLLVILS---KSSPSCPNCKFVHSL 164 (190)
Q Consensus 135 v~~gC~~Clmyvm~~---k~~p~CP~Ck~~v~~ 164 (190)
.--.||+|+.-+-.- ..+-.||+|....-.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 445799997655433 357999999987643
No 65
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=35.47 E-value=29 Score=24.06 Aligned_cols=30 Identities=30% Similarity=0.595 Sum_probs=21.6
Q ss_pred CCeEEeeCccceeee-eecCCC-----CCCCCCCcc
Q 029636 132 NNMVALACMNCHLLV-ILSKSS-----PSCPNCKFV 161 (190)
Q Consensus 132 ~~mv~~gC~~Clmyv-m~~k~~-----p~CP~Ck~~ 161 (190)
..+.|.-|++|++-- |..+.+ -+||.|++.
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred cCceeEECcccchhhcccccccCCceEEEcCCCCCc
Confidence 668889999999755 332433 389999875
No 66
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=35.44 E-value=22 Score=25.59 Aligned_cols=32 Identities=25% Similarity=0.405 Sum_probs=21.0
Q ss_pred CCCeEEeeCccceeeeeecCCCCCCCCCCccc
Q 029636 131 SNNMVALACMNCHLLVILSKSSPSCPNCKFVH 162 (190)
Q Consensus 131 ~~~mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v 162 (190)
....|+|-|-.=..-.=-.+..|.||.||.+.
T Consensus 23 ~G~pVvALCGk~wvp~rdp~~~PVCP~Ck~iy 54 (58)
T PF11238_consen 23 MGTPVVALCGKVWVPTRDPKPFPVCPECKEIY 54 (58)
T ss_pred cCceeEeeeCceeCCCCCCCCCCCCcCHHHHH
Confidence 45688898875333323334568999998653
No 67
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=35.42 E-value=27 Score=23.24 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=22.4
Q ss_pred EeeCccceeeeeecC-CCCCCCCCCcccCC
Q 029636 136 ALACMNCHLLVILSK-SSPSCPNCKFVHSL 164 (190)
Q Consensus 136 ~~gC~~Clmyvm~~k-~~p~CP~Ck~~v~~ 164 (190)
.--|..|..-|-+.. ..-+||+|.+-+..
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIly 31 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYRILY 31 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCceEEE
Confidence 346999999887764 44799999988763
No 68
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=35.11 E-value=27 Score=25.65 Aligned_cols=24 Identities=29% Similarity=0.530 Sum_probs=16.6
Q ss_pred CCCCccchhcccCC------CcceEEeecC
Q 029636 60 DPLPLDWERCLDLQ------SGRMYYFNRK 83 (190)
Q Consensus 60 ~PLPsgWEq~LDlk------SG~iYY~N~~ 83 (190)
..||.||+..+=+. .+.+||+...
T Consensus 5 ~~lp~GW~r~~~~R~~gs~~k~DvyY~sP~ 34 (77)
T cd01396 5 PRLPPGWKRELVPRKSGSAGKFDVYYISPT 34 (77)
T ss_pred CCCCCCCEEEEEEecCCCCCcceEEEECCC
Confidence 34999998755332 3468999765
No 69
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=34.85 E-value=13 Score=33.04 Aligned_cols=27 Identities=26% Similarity=0.602 Sum_probs=19.0
Q ss_pred eeCccceeeee------ecCCC--CCCCCCCcccC
Q 029636 137 LACMNCHLLVI------LSKSS--PSCPNCKFVHS 163 (190)
Q Consensus 137 ~gC~~Clmyvm------~~k~~--p~CP~Ck~~v~ 163 (190)
-.|.+|+|-+= |.+.+ ..||.|..++-
T Consensus 198 ~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy 232 (239)
T COG1579 198 RVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILY 232 (239)
T ss_pred CcccCCeeeecHHHHHHHhcCCCCccCCccchHHH
Confidence 47999999541 22333 79999998764
No 70
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=34.43 E-value=22 Score=27.61 Aligned_cols=26 Identities=31% Similarity=0.687 Sum_probs=17.3
Q ss_pred eeCccceeeeeecC-CCCCCCCCCccc
Q 029636 137 LACMNCHLLVILSK-SSPSCPNCKFVH 162 (190)
Q Consensus 137 ~gC~~Clmyvm~~k-~~p~CP~Ck~~v 162 (190)
.+|.+|.+-+=..+ ....||+|..+.
T Consensus 4 rAC~~C~~I~~~~qf~~~gCpnC~~~l 30 (98)
T cd07973 4 RACLLCSLIKTEDQFERDGCPNCEGYL 30 (98)
T ss_pred chhccCCcccccccccCCCCCCCcchh
Confidence 37999997653222 346899996443
No 71
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=33.90 E-value=27 Score=31.82 Aligned_cols=28 Identities=25% Similarity=0.682 Sum_probs=22.1
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCcccC
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFVHS 163 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v~ 163 (190)
.|--.|+-||--+ ++-.|+|++|++-..
T Consensus 258 ~~GfvCsVCLsvf--c~p~~~C~~C~skF~ 285 (296)
T COG5242 258 LLGFVCSVCLSVF--CRPVPVCKKCKSKFS 285 (296)
T ss_pred EEeeehhhhheee--cCCcCcCcccccccc
Confidence 3445699998755 899999999998654
No 72
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=33.69 E-value=22 Score=28.48 Aligned_cols=30 Identities=23% Similarity=0.508 Sum_probs=24.9
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCcccC
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFVHS 163 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v~ 163 (190)
-+..-|..|.-++-+-..+-.||+|.+...
T Consensus 68 p~~~~C~~C~~~~~~e~~~~~CP~C~s~~~ 97 (115)
T COG0375 68 PAECWCLDCGQEVELEELDYRCPKCGSINL 97 (115)
T ss_pred ccEEEeccCCCeecchhheeECCCCCCCce
Confidence 467789999888888888888999997653
No 73
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=32.80 E-value=21 Score=20.99 Aligned_cols=21 Identities=33% Similarity=0.773 Sum_probs=12.8
Q ss_pred eCccceeeeeecCCCCCCCCCCc
Q 029636 138 ACMNCHLLVILSKSSPSCPNCKF 160 (190)
Q Consensus 138 gC~~Clmyvm~~k~~p~CP~Ck~ 160 (190)
-|++|-- .+....-.||+|..
T Consensus 4 ~Cp~Cg~--~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGA--EIDPDAKFCPNCGA 24 (26)
T ss_pred CCcccCC--cCCcccccChhhCC
Confidence 4666666 35566666777654
No 74
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=30.88 E-value=35 Score=20.68 Aligned_cols=23 Identities=26% Similarity=0.774 Sum_probs=17.7
Q ss_pred CccceeeeeecCCC--CCCCCCCcc
Q 029636 139 CMNCHLLVILSKSS--PSCPNCKFV 161 (190)
Q Consensus 139 C~~Clmyvm~~k~~--p~CP~Ck~~ 161 (190)
|-+|....|.+..- -+|..|..+
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 67888888888754 588888764
No 75
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=30.72 E-value=36 Score=30.19 Aligned_cols=31 Identities=23% Similarity=0.624 Sum_probs=21.4
Q ss_pred CCeEEeeCccce-eee---e---ecC-CCCCCCCCCc-cc
Q 029636 132 NNMVALACMNCH-LLV---I---LSK-SSPSCPNCKF-VH 162 (190)
Q Consensus 132 ~~mv~~gC~~Cl-myv---m---~~k-~~p~CP~Ck~-~v 162 (190)
.++-.+.|..|+ .|. | +.. .-|+||+|.. .+
T Consensus 118 Gsl~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~l 157 (250)
T COG0846 118 GSLKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVL 157 (250)
T ss_pred cceeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCccc
Confidence 558889999996 333 1 222 2489999999 44
No 76
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=29.64 E-value=22 Score=26.40 Aligned_cols=27 Identities=22% Similarity=0.578 Sum_probs=20.5
Q ss_pred eCccceeeeeecCCCCCCCCCCcccCC
Q 029636 138 ACMNCHLLVILSKSSPSCPNCKFVHSL 164 (190)
Q Consensus 138 gC~~Clmyvm~~k~~p~CP~Ck~~v~~ 164 (190)
-|+.|.-.........+|++|......
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCcccc
Confidence 389997766555567899999987654
No 77
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=29.06 E-value=39 Score=31.65 Aligned_cols=28 Identities=29% Similarity=0.820 Sum_probs=21.2
Q ss_pred EeeCccceeeeeecC----CCCCCCCCCcccC
Q 029636 136 ALACMNCHLLVILSK----SSPSCPNCKFVHS 163 (190)
Q Consensus 136 ~~gC~~Clmyvm~~k----~~p~CP~Ck~~v~ 163 (190)
...|+.|-..+=+.. +.-.||||....-
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 457999998876553 3457999998874
No 78
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=28.40 E-value=27 Score=33.55 Aligned_cols=29 Identities=24% Similarity=0.631 Sum_probs=21.2
Q ss_pred eEEeeCccceeeeeecCCCCCCCCCCcccC
Q 029636 134 MVALACMNCHLLVILSKSSPSCPNCKFVHS 163 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~k~~p~CP~Ck~~v~ 163 (190)
--...|.+|+.--. .++.+.||||.+..-
T Consensus 218 ~~~~~C~~C~~~~~-~~~~~~CpRC~~~Ly 246 (418)
T COG2995 218 EGLRSCLCCHYILP-HDAEPRCPRCGSKLY 246 (418)
T ss_pred ccceecccccccCC-HhhCCCCCCCCChhh
Confidence 34567999996554 338899999987543
No 79
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=28.10 E-value=45 Score=26.55 Aligned_cols=30 Identities=23% Similarity=0.393 Sum_probs=24.0
Q ss_pred CeEEeeCccceeeeeecC-CCCCCCCCCccc
Q 029636 133 NMVALACMNCHLLVILSK-SSPSCPNCKFVH 162 (190)
Q Consensus 133 ~mv~~gC~~Clmyvm~~k-~~p~CP~Ck~~v 162 (190)
.+.-.+|+.|.=-|.-.. ....|++|+..+
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCcC
Confidence 689999999988765333 568999999886
No 80
>PRK02935 hypothetical protein; Provisional
Probab=27.67 E-value=43 Score=26.90 Aligned_cols=36 Identities=19% Similarity=0.487 Sum_probs=28.6
Q ss_pred CCeEEeeCccceeee-eecCCCCCCCCCCcccCCCCCC
Q 029636 132 NNMVALACMNCHLLV-ILSKSSPSCPNCKFVHSLPNQQ 168 (190)
Q Consensus 132 ~~mv~~gC~~Clmyv-m~~k~~p~CP~Ck~~v~~~~~~ 168 (190)
..-|.+-||.|+=+- |+-+.| .|..|+...-+|+..
T Consensus 66 tkavqV~CP~C~K~TKmLGrvD-~CM~C~~PLTLd~~l 102 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLGRVD-ACMHCNQPLTLDRSL 102 (110)
T ss_pred ccceeeECCCCCchhhhcccee-ecCcCCCcCCcCccc
Confidence 445778999999877 666655 899999999888764
No 81
>smart00564 PQQ beta-propeller repeat. Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases.
Probab=27.22 E-value=49 Score=18.94 Aligned_cols=18 Identities=22% Similarity=0.680 Sum_probs=15.0
Q ss_pred CcceEEeecCCCCccccC
Q 029636 74 SGRMYYFNRKSSKKSWSL 91 (190)
Q Consensus 74 SG~iYY~N~~T~~ssw~d 91 (190)
.|.+|-+|..||+..|..
T Consensus 15 ~g~l~a~d~~~G~~~W~~ 32 (33)
T smart00564 15 DGTLYALDAKTGEILWTY 32 (33)
T ss_pred CCEEEEEEcccCcEEEEc
Confidence 488999999999888864
No 82
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=26.72 E-value=39 Score=32.50 Aligned_cols=31 Identities=29% Similarity=0.661 Sum_probs=24.3
Q ss_pred CeEEeeCccceeeeeecC----CCCCCCCCCcccC
Q 029636 133 NMVALACMNCHLLVILSK----SSPSCPNCKFVHS 163 (190)
Q Consensus 133 ~mv~~gC~~Clmyvm~~k----~~p~CP~Ck~~v~ 163 (190)
.-=...|+.|-|.+=++. +.-.||||+...-
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCCccc
Confidence 344678999999998876 3368999997764
No 83
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=26.51 E-value=41 Score=25.36 Aligned_cols=29 Identities=28% Similarity=0.306 Sum_probs=19.2
Q ss_pred cccCCCcceEEeecCC--CCccccCCCcccc
Q 029636 69 CLDLQSGRMYYFNRKS--SKKSWSLPENKQK 97 (190)
Q Consensus 69 ~LDlkSG~iYY~N~~T--~~ssw~dPr~~~~ 97 (190)
-+|++|||-||+..-- ..++.-||.-.+=
T Consensus 11 L~DP~SG~Yy~vd~P~Qp~~k~lfDPETGqY 41 (75)
T PF15232_consen 11 LQDPESGQYYVVDAPVQPKTKTLFDPETGQY 41 (75)
T ss_pred eecCCCCCEEEEecCCCcceeeeecCCCCcE
Confidence 5799999999997433 3445556653333
No 84
>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=26.43 E-value=20 Score=36.73 Aligned_cols=25 Identities=16% Similarity=0.385 Sum_probs=17.7
Q ss_pred eCccceeeee-e---cCCCCCCCCCCccc
Q 029636 138 ACMNCHLLVI-L---SKSSPSCPNCKFVH 162 (190)
Q Consensus 138 gC~~Clmyvm-~---~k~~p~CP~Ck~~v 162 (190)
-|+||-.|.- + ...+.-|+||..++
T Consensus 882 kC~RCW~~~~~~~~~~~~~~~C~rC~~~~ 910 (912)
T PRK05743 882 KCERCWHYREDVGSDAEHPTLCGRCVSNV 910 (912)
T ss_pred CCCCcCCEeCCcCCCCCCCCcChhHHHHh
Confidence 5999999983 2 22345799998765
No 85
>PF11008 DUF2846: Protein of unknown function (DUF2846); InterPro: IPR022548 Some members in this group of proteins with unknown function are annotated as lipoproteins. However this cannot be confirmed.
Probab=26.21 E-value=61 Score=24.61 Aligned_cols=20 Identities=15% Similarity=0.371 Sum_probs=14.7
Q ss_pred cchhcccCCCcceEEeecCC
Q 029636 65 DWERCLDLQSGRMYYFNRKS 84 (190)
Q Consensus 65 gWEq~LDlkSG~iYY~N~~T 84 (190)
...--++.+.|++||++..-
T Consensus 84 ~~~l~~~~~~G~~yy~r~~~ 103 (117)
T PF11008_consen 84 ANSLDVTVEAGKTYYVRQDI 103 (117)
T ss_pred ccEEEEEEcCCCEEEEEEEe
Confidence 35567788889999997544
No 86
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=25.85 E-value=69 Score=30.08 Aligned_cols=29 Identities=28% Similarity=0.689 Sum_probs=23.5
Q ss_pred cchhcccCCCcceEEeecCCCCccccCCCc
Q 029636 65 DWERCLDLQSGRMYYFNRKSSKKSWSLPEN 94 (190)
Q Consensus 65 gWEq~LDlkSG~iYY~N~~T~~ssw~dPr~ 94 (190)
.|-.-... +|-.||.|..|+++.|..|+.
T Consensus 152 ~wv~~Kne-s~~~yy~n~~t~esvwk~P~~ 180 (336)
T KOG0150|consen 152 EWVEGKNE-SGPTYYSNKRTNESVWKPPRI 180 (336)
T ss_pred hcccccCC-CCCCcceecCCCccccCCCCc
Confidence 45555554 388899999999999999994
No 87
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=25.77 E-value=54 Score=21.36 Aligned_cols=25 Identities=28% Similarity=0.721 Sum_probs=15.9
Q ss_pred EeeCcccee-eeeecC----CCCCCCCCCc
Q 029636 136 ALACMNCHL-LVILSK----SSPSCPNCKF 160 (190)
Q Consensus 136 ~~gC~~Clm-yvm~~k----~~p~CP~Ck~ 160 (190)
.--|..|-- +..+.. ....||+|.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 346888876 433322 2358999998
No 88
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=25.59 E-value=41 Score=28.17 Aligned_cols=27 Identities=26% Similarity=0.664 Sum_probs=16.5
Q ss_pred EeeCccceeee-----eecCCCCCCCCCCccc
Q 029636 136 ALACMNCHLLV-----ILSKSSPSCPNCKFVH 162 (190)
Q Consensus 136 ~~gC~~Clmyv-----m~~k~~p~CP~Ck~~v 162 (190)
...|..|.--+ +.....|+||+|+..+
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~l 140 (224)
T cd01412 109 RVRCSSCGYVGENNEEIPEEELPRCPKCGGLL 140 (224)
T ss_pred ccccCCCCCCCCcchhhhccCCCCCCCCCCcc
Confidence 34477775321 2234469999998755
No 89
>PLN02843 isoleucyl-tRNA synthetase
Probab=25.55 E-value=30 Score=35.96 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=19.6
Q ss_pred eCccceeeee-ecC---CCCCCCCCCcccC
Q 029636 138 ACMNCHLLVI-LSK---SSPSCPNCKFVHS 163 (190)
Q Consensus 138 gC~~Clmyvm-~~k---~~p~CP~Ck~~v~ 163 (190)
-|+||-.|.= +-. ...-|+||..++-
T Consensus 934 kC~RCW~~~~~~~~~~~~~~lC~rc~~~~~ 963 (974)
T PLN02843 934 KCERCWNYSPAVGSFSDHPTLCERCYPVVI 963 (974)
T ss_pred CCCCCCCEeCCcCCCCCCCCcChhhHHHHc
Confidence 6999999993 311 2247999999986
No 90
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=25.05 E-value=37 Score=26.69 Aligned_cols=17 Identities=35% Similarity=0.917 Sum_probs=12.4
Q ss_pred EeeCccceeeeeecCCCCCCCCCCcc
Q 029636 136 ALACMNCHLLVILSKSSPSCPNCKFV 161 (190)
Q Consensus 136 ~~gC~~Clmyvm~~k~~p~CP~Ck~~ 161 (190)
-.-|++||+- ||+|+|.
T Consensus 67 ~~~C~GC~~P---------C~~C~S~ 83 (103)
T PF14949_consen 67 DEDCPGCHYP---------CPKCGSR 83 (103)
T ss_pred CCCCCCcccc---------CCCCCCC
Confidence 3568999874 8888774
No 91
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=24.69 E-value=51 Score=31.09 Aligned_cols=28 Identities=29% Similarity=0.839 Sum_probs=20.6
Q ss_pred eeCccceeeeeecC----CCCCCCCCCcccCC
Q 029636 137 LACMNCHLLVILSK----SSPSCPNCKFVHSL 164 (190)
Q Consensus 137 ~gC~~Clmyvm~~k----~~p~CP~Ck~~v~~ 164 (190)
..|+.|-..+=+.. +.-.||||....-.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 45999998875553 33579999998743
No 92
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=24.60 E-value=89 Score=26.41 Aligned_cols=35 Identities=23% Similarity=0.574 Sum_probs=24.8
Q ss_pred CCeEEeeCccce------eeeeecCCC-CCCCCCCcccCCCCC
Q 029636 132 NNMVALACMNCH------LLVILSKSS-PSCPNCKFVHSLPNQ 167 (190)
Q Consensus 132 ~~mv~~gC~~Cl------myvm~~k~~-p~CP~Ck~~v~~~~~ 167 (190)
..+..+|| .|. +.+-|-|.+ ++||.|....-+-+.
T Consensus 107 ~d~RiVGC-~c~eD~~~V~Wmwl~Kge~~rc~eCG~~fkL~~v 148 (153)
T KOG3352|consen 107 YDKRIVGC-GCEEDSHAVVWMWLEKGETQRCPECGHYFKLVPV 148 (153)
T ss_pred CCceEEee-cccCCCcceEEEEEEcCCcccCCcccceEEeeec
Confidence 45678999 774 445577755 799999988765444
No 93
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=23.91 E-value=26 Score=29.61 Aligned_cols=37 Identities=32% Similarity=0.352 Sum_probs=0.0
Q ss_pred ccccccccccceeeecccCCCCcccCCCCcCCceeee
Q 029636 3 MELTELSLAPTHCVVVDKSNSSSESEDNPSRKRKFLS 39 (190)
Q Consensus 3 m~~~elsl~p~~~~~~~~~~ssse~~~~~~~~R~~~~ 39 (190)
+|=+||-||+-|........+++......+.+|.|..
T Consensus 3 ~~~TELrLGLPG~~~~~~~~~~~~~~~~~~~kR~F~~ 39 (215)
T PF02309_consen 3 LKATELRLGLPGSESPDASSSSSSKKSSSGNKRGFSE 39 (215)
T ss_dssp -------------------------------------
T ss_pred chhhhhcccCCCCCCCCcccccccccccCcccccchh
Confidence 5669999998876644322233334456788888865
No 94
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.29 E-value=38 Score=23.07 Aligned_cols=28 Identities=14% Similarity=0.284 Sum_probs=17.6
Q ss_pred eEEeeCccceeeee-ecCCCCCCCCCCcc
Q 029636 134 MVALACMNCHLLVI-LSKSSPSCPNCKFV 161 (190)
Q Consensus 134 mv~~gC~~Clmyvm-~~k~~p~CP~Ck~~ 161 (190)
++..-||+|---+| ..+..-.|.+|..+
T Consensus 18 ~~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred EccCcCcCCCcchheccCCcEECCCcCCE
Confidence 45557888866333 23345788888764
No 95
>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional
Probab=23.01 E-value=22 Score=36.77 Aligned_cols=26 Identities=8% Similarity=-0.038 Sum_probs=18.6
Q ss_pred eCccceeeeeec----CCCCCCCCCCcccC
Q 029636 138 ACMNCHLLVILS----KSSPSCPNCKFVHS 163 (190)
Q Consensus 138 gC~~Clmyvm~~----k~~p~CP~Ck~~v~ 163 (190)
-|+||-.|.--- +.+.-|+||..++-
T Consensus 924 kC~RCw~~~~~~~~~~~~~~lC~rC~~~~~ 953 (961)
T PRK13804 924 KCARSWRITPDVGSDPYYPDVSPRDAKALR 953 (961)
T ss_pred CCcCCCCCcCCcCCCCCCCCcChhHHHHHH
Confidence 599999998422 22357999988764
No 96
>PF14435 SUKH-4: SUKH-4 immunity protein
Probab=22.73 E-value=51 Score=26.31 Aligned_cols=20 Identities=25% Similarity=0.506 Sum_probs=15.7
Q ss_pred cchhcccCCCcceEEeecCC
Q 029636 65 DWERCLDLQSGRMYYFNRKS 84 (190)
Q Consensus 65 gWEq~LDlkSG~iYY~N~~T 84 (190)
+..=|+|..||+||+++...
T Consensus 86 ~~~i~ld~~tG~V~~~~~~~ 105 (179)
T PF14435_consen 86 GGSICLDPATGAVYALDPDE 105 (179)
T ss_pred CCeEEEECCCCeEEEecCCc
Confidence 33348999999999997665
No 97
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=22.41 E-value=54 Score=27.91 Aligned_cols=29 Identities=24% Similarity=0.327 Sum_probs=18.4
Q ss_pred eEEeeCccceeeeeec--CCCCCCCCCCccc
Q 029636 134 MVALACMNCHLLVILS--KSSPSCPNCKFVH 162 (190)
Q Consensus 134 mv~~gC~~Clmyvm~~--k~~p~CP~Ck~~v 162 (190)
+-...|..|..-+-.. ...|+||+|...+
T Consensus 116 ~~~~~C~~C~~~~~~~~~~~~p~C~~Cgg~l 146 (225)
T cd01411 116 LYRIYCTVCGKTVDWEEYLKSPYHAKCGGVI 146 (225)
T ss_pred cCeeEeCCCCCccchhhcCCCCCCCCCCCEe
Confidence 4445688887543211 2359999998765
No 98
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=21.61 E-value=54 Score=21.06 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=10.8
Q ss_pred cCCCCCCCCCCccc
Q 029636 149 SKSSPSCPNCKFVH 162 (190)
Q Consensus 149 ~k~~p~CP~Ck~~v 162 (190)
.+.+-+||+|.+..
T Consensus 2 a~i~v~CP~C~s~~ 15 (36)
T PF03811_consen 2 AKIDVHCPRCQSTE 15 (36)
T ss_pred CcEeeeCCCCCCCC
Confidence 35567899998887
No 99
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=21.35 E-value=71 Score=19.95 Aligned_cols=26 Identities=23% Similarity=0.720 Sum_probs=20.2
Q ss_pred eeCccceeeeeecCCC--CCCCCCCccc
Q 029636 137 LACMNCHLLVILSKSS--PSCPNCKFVH 162 (190)
Q Consensus 137 ~gC~~Clmyvm~~k~~--p~CP~Ck~~v 162 (190)
..|.+|-+..|.+..- -+|.-|..+.
T Consensus 2 ~~C~~C~t~L~yP~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASSVRCALCQTVN 29 (31)
T ss_pred cCcCCCCcEeecCCCCCeEECCCCCeEe
Confidence 3688898888888855 5899998764
No 100
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=21.05 E-value=50 Score=24.65 Aligned_cols=20 Identities=30% Similarity=0.413 Sum_probs=10.0
Q ss_pred CCCccchhcccCCCcceEEe
Q 029636 61 PLPLDWERCLDLQSGRMYYF 80 (190)
Q Consensus 61 PLPsgWEq~LDlkSG~iYY~ 80 (190)
-||.+.-...|-.+|++||+
T Consensus 11 ~lP~NLy~~~dkr~~k~Yy~ 30 (75)
T PF09003_consen 11 DLPPNLYCRKDKRNGKGYYQ 30 (75)
T ss_dssp GS-TTEEEETT-----SEEE
T ss_pred CCCCCccccCCcCcceeEEE
Confidence 36777667778888999884
No 101
>PRK12496 hypothetical protein; Provisional
Probab=20.97 E-value=53 Score=27.08 Aligned_cols=26 Identities=15% Similarity=0.252 Sum_probs=19.2
Q ss_pred eeCccceeeeeecCCCCCCCCCCccc
Q 029636 137 LACMNCHLLVILSKSSPSCPNCKFVH 162 (190)
Q Consensus 137 ~gC~~Clmyvm~~k~~p~CP~Ck~~v 162 (190)
--|++|-=++-.....-.||.|.+-+
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChh
Confidence 56999986665555556799999754
No 102
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.79 E-value=91 Score=20.09 Aligned_cols=24 Identities=29% Similarity=0.699 Sum_probs=14.8
Q ss_pred eeCccceee--eeec--C-CCCCCCCCCc
Q 029636 137 LACMNCHLL--VILS--K-SSPSCPNCKF 160 (190)
Q Consensus 137 ~gC~~Clmy--vm~~--k-~~p~CP~Ck~ 160 (190)
-.|..|--. ++.+ + ....||+|..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 357778622 2322 2 3479999987
No 103
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=20.70 E-value=32 Score=21.73 Aligned_cols=28 Identities=18% Similarity=0.570 Sum_probs=14.6
Q ss_pred eCccceeeeeecCCCCC---CCCCCcccCCC
Q 029636 138 ACMNCHLLVILSKSSPS---CPNCKFVHSLP 165 (190)
Q Consensus 138 gC~~Clmyvm~~k~~p~---CP~Ck~~v~~~ 165 (190)
-||.|--.....+.... |++|....+.+
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPIS 33 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-S
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCCC
Confidence 37777433333333333 88888877653
No 104
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.62 E-value=47 Score=21.14 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=6.3
Q ss_pred CCCCCCcc
Q 029636 154 SCPNCKFV 161 (190)
Q Consensus 154 ~CP~Ck~~ 161 (190)
+||+|+..
T Consensus 1 ~CP~C~~~ 8 (41)
T PF13453_consen 1 KCPRCGTE 8 (41)
T ss_pred CcCCCCcc
Confidence 69999873
No 105
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.33 E-value=60 Score=23.76 Aligned_cols=13 Identities=23% Similarity=0.761 Sum_probs=10.0
Q ss_pred CCCCCCCCCCccc
Q 029636 150 KSSPSCPNCKFVH 162 (190)
Q Consensus 150 k~~p~CP~Ck~~v 162 (190)
+....||+|+++.
T Consensus 3 ~~~~~CPRC~S~n 15 (63)
T PF02701_consen 3 EQPLPCPRCDSTN 15 (63)
T ss_pred ccCCCCCCcCCCC
Confidence 3456899999865
No 106
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=20.27 E-value=55 Score=21.64 Aligned_cols=29 Identities=21% Similarity=0.462 Sum_probs=21.9
Q ss_pred CCCeEEeeCccceeeeeecC-CCCCCCCCC
Q 029636 131 SNNMVALACMNCHLLVILSK-SSPSCPNCK 159 (190)
Q Consensus 131 ~~~mv~~gC~~Clmyvm~~k-~~p~CP~Ck 159 (190)
+..|...-|+.|-+-.|=.+ ..--||.|.
T Consensus 12 G~~ML~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 12 GWTMLDEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred hHhHhcCccCCCCCeeEEecCCCEECCCCC
Confidence 35688899999987777644 557899884
Done!