Query 024500
Match_columns 266
No_of_seqs 187 out of 1146
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 05:03:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024500.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024500hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10353 3-methyl-adenine DNA 100.0 6.2E-51 1.3E-55 356.2 11.8 105 159-265 1-105 (187)
2 TIGR00624 tag DNA-3-methyladen 100.0 1.5E-50 3.2E-55 351.7 11.7 104 160-265 1-104 (179)
3 COG2818 Tag 3-methyladenine DN 100.0 8.5E-49 1.8E-53 343.1 11.2 106 159-265 1-106 (188)
4 PF03352 Adenine_glyco: Methyl 100.0 3E-47 6.4E-52 330.9 9.6 100 164-265 1-100 (179)
5 cd00056 ENDO3c endonuclease II 93.7 0.39 8.5E-06 39.5 7.9 69 192-264 1-69 (158)
6 PRK10702 endonuclease III; Pro 91.1 1.7 3.6E-05 39.0 9.0 70 191-264 29-98 (211)
7 PF00730 HhH-GPD: HhH-GPD supe 91.1 1.2 2.6E-05 34.3 7.1 63 199-263 4-66 (108)
8 TIGR01083 nth endonuclease III 90.0 1.8 3.9E-05 37.6 8.1 70 191-264 26-95 (191)
9 TIGR03252 uncharacterized HhH- 88.0 4.4 9.5E-05 36.2 9.1 73 191-264 18-93 (177)
10 PRK13913 3-methyladenine DNA g 84.6 7.8 0.00017 35.3 9.1 72 191-264 30-106 (218)
11 smart00478 ENDO3c endonuclease 84.5 3.7 8E-05 33.5 6.4 57 204-264 5-61 (149)
12 PRK10880 adenine DNA glycosyla 82.2 9.2 0.0002 37.1 9.1 69 191-264 30-98 (350)
13 TIGR01084 mutY A/G-specific ad 81.1 8.6 0.00019 36.0 8.2 69 191-264 26-94 (275)
14 cd00166 SAM Sterile alpha moti 68.4 14 0.0003 25.1 4.7 43 214-258 17-61 (63)
15 COG0177 Nth Predicted EndoIII- 66.3 38 0.00082 31.1 8.3 69 191-264 29-98 (211)
16 COG1393 ArsC Arsenate reductas 63.8 8 0.00017 31.9 3.2 47 199-248 47-93 (117)
17 COG0122 AlkA 3-methyladenine D 60.8 51 0.0011 31.1 8.3 70 189-264 103-180 (285)
18 PF00536 SAM_1: SAM domain (St 57.4 26 0.00057 24.6 4.6 43 214-258 18-62 (64)
19 PF13495 Phage_int_SAM_4: Phag 50.5 76 0.0016 22.9 6.2 52 191-242 1-52 (85)
20 PF07647 SAM_2: SAM domain (St 49.7 30 0.00066 24.3 3.9 43 214-258 19-64 (66)
21 PRK01229 N-glycosylase/DNA lya 48.9 52 0.0011 30.0 6.1 67 187-261 33-99 (208)
22 PF14493 HTH_40: Helix-turn-he 36.7 1.3E+02 0.0029 23.0 5.9 46 194-241 4-60 (91)
23 PRK10308 3-methyl-adenine DNA 36.6 2E+02 0.0044 27.0 8.1 79 180-264 102-191 (283)
24 COG2231 Uncharacterized protei 34.8 1.5E+02 0.0033 27.6 6.9 83 171-258 14-97 (215)
25 cd03036 ArsC_like Arsenate Red 34.0 41 0.0009 26.7 2.8 57 189-248 35-93 (111)
26 cd00052 EH Eps15 homology doma 32.8 24 0.00053 24.0 1.1 27 216-242 1-27 (67)
27 PHA02543 regA translation repr 32.5 15 0.00033 31.5 0.0 59 192-251 54-112 (125)
28 PRK01172 ski2-like helicase; P 32.2 65 0.0014 33.0 4.5 38 224-266 635-672 (674)
29 smart00454 SAM Sterile alpha m 31.1 1.6E+02 0.0034 19.9 5.0 43 216-260 21-66 (68)
30 PF02173 pKID: pKID domain; I 28.9 17 0.00036 25.9 -0.2 17 207-223 13-29 (41)
31 KOG2846 Predicted membrane pro 27.8 1.9E+02 0.0041 28.5 6.6 76 187-266 22-110 (328)
32 KOG0898 40S ribosomal protein 27.0 72 0.0016 28.2 3.3 32 210-241 13-45 (152)
33 PF12583 TPPII_N: Tripeptidyl 26.9 36 0.00079 29.7 1.4 29 211-239 70-98 (139)
34 cd02977 ArsC_family Arsenate R 25.2 58 0.0013 25.2 2.2 46 199-248 45-92 (105)
35 cd03034 ArsC_ArsC Arsenate Red 24.4 1.3E+02 0.0028 24.0 4.1 44 200-248 46-91 (112)
36 PF09317 DUF1974: Domain of un 24.2 1E+02 0.0022 29.4 4.0 68 171-250 114-199 (284)
37 cd05027 S-100B S-100B: S-100B 23.9 55 0.0012 25.3 1.8 47 213-259 7-60 (88)
38 PRK13344 spxA transcriptional 23.3 58 0.0012 27.1 1.9 44 200-247 47-91 (132)
39 PF12415 rpo132: Poxvirus DNA 23.2 76 0.0017 21.6 2.1 14 251-264 18-31 (33)
40 PF03960 ArsC: ArsC family; I 22.7 52 0.0011 25.9 1.5 45 200-248 43-89 (110)
41 PRK10026 arsenate reductase; P 22.6 1.3E+02 0.0028 25.8 3.9 43 201-248 50-94 (141)
42 PRK04038 rps19p 30S ribosomal 22.5 72 0.0016 27.7 2.4 24 219-242 8-31 (134)
43 TIGR01617 arsC_related transcr 21.6 83 0.0018 25.0 2.5 56 190-248 36-93 (117)
44 cd03032 ArsC_Spx Arsenate Redu 21.3 1.8E+02 0.0039 23.1 4.4 45 200-248 47-92 (115)
45 PF14534 DUF4440: Domain of un 20.6 95 0.0021 22.2 2.4 48 209-257 1-48 (107)
46 PF05075 DUF684: Protein of un 20.6 1.9E+02 0.004 27.8 5.0 40 188-227 115-161 (345)
No 1
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=100.00 E-value=6.2e-51 Score=356.18 Aligned_cols=105 Identities=41% Similarity=0.778 Sum_probs=102.8
Q ss_pred CCCCCCCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 024500 159 KKRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLA 238 (266)
Q Consensus 159 ~~RC~Wat~~sdply~~YHDeEWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~ 238 (266)
+.||.|++ +||+|++|||+|||+|+|||++|||+|+||+|||||||.|||+||++||+||++|||++||+|+|++|++
T Consensus 1 m~rC~W~~--~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~ 78 (187)
T PRK10353 1 MERCGWVS--QDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVER 78 (187)
T ss_pred CCCCCCCC--CChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHH
Confidence 36999996 8999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccchhhcchhHHHHHHHHHHHHHhh
Q 024500 239 AGSAASSLLSELKLRAIIENARQISKV 265 (266)
Q Consensus 239 L~~d~~IIRNr~KIrAVI~NArailkI 265 (266)
||+|++|||||+||+|||+||+++++|
T Consensus 79 Ll~d~~IIRnr~KI~Avi~NA~~~l~i 105 (187)
T PRK10353 79 LVQDAGIIRHRGKIQAIIGNARAYLQM 105 (187)
T ss_pred HhcCchhHHhHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999987
No 2
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.5e-50 Score=351.67 Aligned_cols=104 Identities=36% Similarity=0.706 Sum_probs=102.0
Q ss_pred CCCCCCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 024500 160 KRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAA 239 (266)
Q Consensus 160 ~RC~Wat~~sdply~~YHDeEWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L 239 (266)
.||.|++ +||+|++|||+|||+|+|||+.|||+|+||+|||||||.|||+||++||+||+||||++||+|+|++|++|
T Consensus 1 ~rC~W~~--~~~l~~~YHD~eWG~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L 78 (179)
T TIGR00624 1 VRCGWAS--VDPLYRAYHDNEWGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERL 78 (179)
T ss_pred CCCCCcC--CChHHHHhhhccCCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHH
Confidence 4899996 79999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhhcchhHHHHHHHHHHHHHhh
Q 024500 240 GSAASSLLSELKLRAIIENARQISKV 265 (266)
Q Consensus 240 ~~d~~IIRNr~KIrAVI~NArailkI 265 (266)
|+|++|||||+||+|||+||+++++|
T Consensus 79 ~~d~~IIRnr~KI~Avi~NA~~~l~i 104 (179)
T TIGR00624 79 LQDDGIIRNRGKIEATIANARAALQL 104 (179)
T ss_pred hcCccchhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999986
No 3
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=8.5e-49 Score=343.13 Aligned_cols=106 Identities=44% Similarity=0.827 Sum_probs=102.6
Q ss_pred CCCCCCCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 024500 159 KKRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLA 238 (266)
Q Consensus 159 ~~RC~Wat~~sdply~~YHDeEWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~ 238 (266)
+.||.|+. +.||+|.+|||+|||+|++||+.|||+||||+|||||||.|||+||++||+||++|||++||.|+|++|++
T Consensus 1 ~~rC~w~~-~~~ply~~YHD~eWG~p~~Dd~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~Fd~~kVA~~~~~dver 79 (188)
T COG2818 1 MNRCAWAG-GLDPLYLAYHDTEWGVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFREAFHGFDPEKVAAMTEEDVER 79 (188)
T ss_pred CCcccccC-CCCchhhcccccccCCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhcCCHHHHHcCCHHHHHH
Confidence 46999996 34899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccchhhcchhHHHHHHHHHHHHHhh
Q 024500 239 AGSAASSLLSELKLRAIIENARQISKV 265 (266)
Q Consensus 239 L~~d~~IIRNr~KIrAVI~NArailkI 265 (266)
||+|++|||||+||.|||+||+++++|
T Consensus 80 Ll~d~gIIR~r~KI~A~i~NA~~~l~l 106 (188)
T COG2818 80 LLADAGIIRNRGKIKATINNARAVLEL 106 (188)
T ss_pred HHhCcchhhhHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999986
No 4
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=100.00 E-value=3e-47 Score=330.89 Aligned_cols=100 Identities=49% Similarity=0.907 Sum_probs=90.3
Q ss_pred CCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccc
Q 024500 164 WVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAA 243 (266)
Q Consensus 164 Wat~~sdply~~YHDeEWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~ 243 (266)
|+. ++|+|++|||+|||+|+|||++|||+|+||+|||||||.+||+||++||+||+||||++||+|+|++|++||+|+
T Consensus 1 W~~--~~~~~~~YHD~eWG~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~ 78 (179)
T PF03352_consen 1 WAN--SDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDP 78 (179)
T ss_dssp TTT--SSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTST
T ss_pred CCC--CChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCc
Confidence 885 799999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcchhHHHHHHHHHHHHHhh
Q 024500 244 SSLLSELKLRAIIENARQISKV 265 (266)
Q Consensus 244 ~IIRNr~KIrAVI~NArailkI 265 (266)
+|||||+||+|||+||++|++|
T Consensus 79 ~iIRnr~KI~Avi~NA~~~l~i 100 (179)
T PF03352_consen 79 GIIRNRRKIRAVINNARAILKI 100 (179)
T ss_dssp TSS--HHHHHHHHHHHHHHHHH
T ss_pred chhhhHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999987
No 5
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=93.72 E-value=0.39 Score=39.48 Aligned_cols=69 Identities=23% Similarity=0.139 Sum_probs=58.1
Q ss_pred HHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 192 FELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 192 FE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
||.|+=.++..-.+|..+.+-...|.+.|. .+++.|+..+++++.++...-+ .+.|.+.|++=|+.+.+
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g-pt~~~l~~~~~~~l~~~~~~~G---~~~kA~~i~~~a~~~~~ 69 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG-PTPEALAAADEEELRELIRSLG---YRRKAKYLKELARAIVE 69 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC-CCHHHHHCCCHHHHHHHHHhcC---hHHHHHHHHHHHHHHHH
Confidence 678888888888999999988888888875 7999999999999988766544 47799999988888764
No 6
>PRK10702 endonuclease III; Provisional
Probab=91.14 E-value=1.7 Score=39.02 Aligned_cols=70 Identities=17% Similarity=0.095 Sum_probs=54.5
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
-||.|+-++..+-=+|..|.+--+.|.+.| .+++.+++.++++|+++...-+. .+.|-+.+++.|+.+++
T Consensus 29 p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~--pt~e~l~~a~~~~l~~~i~~~G~--y~~kA~~l~~~a~~i~~ 98 (211)
T PRK10702 29 PFELLIAVLLSAQATDVSVNKATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGL--YNSKAENVIKTCRILLE 98 (211)
T ss_pred hHHHHHHHHHHhhcCHHHHHHHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCC--HHHHHHHHHHHHHHHHH
Confidence 599999999998999999987777666544 48999999999999987665443 34466677777777765
No 7
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=91.13 E-value=1.2 Score=34.33 Aligned_cols=63 Identities=22% Similarity=0.045 Sum_probs=52.0
Q ss_pred HHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHH
Q 024500 199 GALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQIS 263 (266)
Q Consensus 199 gfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArail 263 (266)
++..-.+|..+.+-...|.+.|...+++.|+..++++|.++... .--++.|-+.|++=|+.++
T Consensus 4 Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~--~G~~~~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 4 ILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRP--LGFSRRKAKYIIELARAIL 66 (108)
T ss_dssp HHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTT--STSHHHHHHHHHHHHHHHH
T ss_pred eecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhc--cCCCHHHHHHHHHHHHHhh
Confidence 44556789999999999999999999999999999999998766 3456678888988888774
No 8
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=90.02 E-value=1.8 Score=37.55 Aligned_cols=70 Identities=21% Similarity=0.157 Sum_probs=55.3
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
-||.|+-++.-.--+|..+.+--..|.+.| .+++.|+..+++++++++..-+. .+.|.+.|++=|+++++
T Consensus 26 pf~~Li~~ILsqqt~~~~~~~~~~~l~~~~--pt~~~l~~~~~~~L~~~ir~~G~--~~~Ka~~i~~~a~~i~~ 95 (191)
T TIGR01083 26 PFELLVATILSAQATDKSVNKATKKLFEVY--PTPQALAQAGLEELEEYIKSIGL--YRNKAKNIIALCRILVE 95 (191)
T ss_pred HHHHHHHHHHHhhCcHHHHHHHHHHHHHHC--CCHHHHHcCCHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHH
Confidence 599999999988999999988777776655 48999999999999887655443 45777778777777653
No 9
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=88.00 E-value=4.4 Score=36.21 Aligned_cols=73 Identities=12% Similarity=0.057 Sum_probs=54.3
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHH-HHhcCCCHHHHhcCCHHHHHHhccc-chhhc-chhHHHHHHHHHHHHHh
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFR-EVFVGFDPIAVSKLNEKKLLAAGSA-ASSLL-SELKLRAIIENARQISK 264 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FR-eAF~~FDp~kVA~~~E~~Ie~L~~d-~~IIR-Nr~KIrAVI~NArailk 264 (266)
-||+|+--+.-+--+|..+.+--+.+. ++|. .||+.|+.++.++|++++.. +++.+ .+.|=+-|++=|+.|++
T Consensus 18 pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~-~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie 93 (177)
T TIGR03252 18 PFALLTGMLLDQQVPMERAFAGPHKIARRMGS-LDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVD 93 (177)
T ss_pred hHHHHHHHHHhccCcHHHHHHHHHHHHHHhCC-CCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHH
Confidence 499999999999999999886666664 4544 89999999999999998753 23222 34666667666666654
No 10
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=84.59 E-value=7.8 Score=35.31 Aligned_cols=72 Identities=15% Similarity=0.200 Sum_probs=55.2
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHHHHhc-----CCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFREVFV-----GFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~-----~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
-||.|+-.+.-.-=+|..+.+--+.+++.|. .-+|+.|+..++++|+++....+ -.++|.+.+.+=|+.|++
T Consensus 30 ~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~G--f~~~KA~~Lk~la~~i~~ 106 (218)
T PRK13913 30 KFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSG--FYNQKAKRLIDLSENILK 106 (218)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHH
Confidence 3898888887777889888877666766653 23899999999999999877655 456777888777777754
No 11
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=84.53 E-value=3.7 Score=33.49 Aligned_cols=57 Identities=19% Similarity=0.152 Sum_probs=45.6
Q ss_pred CcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 204 LTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 204 LSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
.+|..+.+-...|.+.|- +|+.|+..++++|++++..-+ -...|.+.|++.|+.+.+
T Consensus 5 ~~~~~a~~~~~~l~~~~~--~~~~l~~~~~~eL~~~l~~~g--~~~~ka~~i~~~a~~~~~ 61 (149)
T smart00478 5 TSDEAVNKATERLFEKFP--TPEDLAAADEEELEELIRPLG--FYRRKAKYLIELARILVE 61 (149)
T ss_pred ccHHHHHHHHHHHHHHCC--CHHHHHCCCHHHHHHHHHHcC--ChHHHHHHHHHHHHHHHH
Confidence 567778887788888876 899999999999988766522 456799999999988764
No 12
>PRK10880 adenine DNA glycosylase; Provisional
Probab=82.23 E-value=9.2 Score=37.14 Aligned_cols=69 Identities=10% Similarity=0.115 Sum_probs=56.5
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
-|+.|+-|++..--+|.+++.--+.|.+.| .|++.+|..++++|..+...-+.- .|.+-+..-|+.+.+
T Consensus 30 py~ilVseILlQQT~v~~v~~~~~rl~~~f--Pt~~~La~a~~eel~~~~~glGyy---~RAr~L~~~A~~i~~ 98 (350)
T PRK10880 30 PYKVWLSEVMLQQTQVATVIPYFERFMARF--PTVTDLANAPLDEVLHLWTGLGYY---ARARNLHKAAQQVAT 98 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHC--cCHHHHHCcCHHHHHHHHHcCChH---HHHHHHHHHHHHHHH
Confidence 489999999999999999999888888876 579999999999999887766653 266777777776643
No 13
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=81.07 E-value=8.6 Score=35.96 Aligned_cols=69 Identities=12% Similarity=0.141 Sum_probs=56.2
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
.|+.|+-+++..--+|.+++.-.+.|.+.| -+++.|+..++++|..+...-+.- .|.+.+.+=|+.|.+
T Consensus 26 py~vlvseIL~QQT~v~~v~~~~~rl~~~f--pt~~~La~a~~eeL~~~~~~lG~y---~RAr~L~~~A~~i~~ 94 (275)
T TIGR01084 26 PYRVWLSEVMLQQTQVATVIPYFERFLERF--PTVQALANAPQDEVLKLWEGLGYY---ARARNLHKAAQEVVE 94 (275)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHhC--CCHHHHHCcCHHHHHHHHHHCCcH---HHHHHHHHHHHHHHH
Confidence 589999999999999999999888888887 579999999999998876665653 256666666666654
No 14
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=68.41 E-value=14 Score=25.12 Aligned_cols=43 Identities=21% Similarity=0.196 Sum_probs=32.7
Q ss_pred HHHHHHh--cCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHH
Q 024500 214 HIFREVF--VGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (266)
Q Consensus 214 e~FReAF--~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~N 258 (266)
+.|.+.| .+||-..+..++++++..+.... .-+|.||...|.+
T Consensus 17 ~~y~~~f~~~~i~g~~L~~l~~~dL~~lgi~~--~g~r~~i~~~i~~ 61 (63)
T cd00166 17 GQYADNFRENGIDGDLLLLLTEEDLKELGITL--PGHRKKILKAIQK 61 (63)
T ss_pred HHHHHHHHHcCCCHHHHhHCCHHHHHHcCCCC--HHHHHHHHHHHHH
Confidence 6677777 56889999999999999766532 4677888776654
No 15
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=66.28 E-value=38 Score=31.06 Aligned_cols=69 Identities=23% Similarity=0.182 Sum_probs=47.1
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCC-HHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHh
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFD-PIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FD-p~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailk 264 (266)
-||+|+--+..+-=+=..+- .++++.|.-|+ |+.++..++++|+++...-+ ..+.|-+.|+.=|+.+++
T Consensus 29 pf~lLva~iLSaqttD~~vn---~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iG--lyr~KAk~I~~~~~~l~e 98 (211)
T COG0177 29 PFELLVAVILSAQTTDEVVN---KATPALFKRYPTPEDLLNADEEELEELIKSIG--LYRNKAKNIKELARILLE 98 (211)
T ss_pred cHHHHHHHHHhccCchHHHH---HHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcC--CcHHHHHHHHHHHHHHHH
Confidence 47877643333322211111 45666677676 99999999999999988655 556677788888888875
No 16
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=63.77 E-value=8 Score=31.91 Aligned_cols=47 Identities=9% Similarity=-0.156 Sum_probs=36.5
Q ss_pred HHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcc
Q 024500 199 GALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLS 248 (266)
Q Consensus 199 gfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRN 248 (266)
..+.|..|..+++++..+-+... .++....+++.++.|+.++.+|+-
T Consensus 47 l~~~g~~~~~li~t~~~~~r~L~---~~~~~~~~~~~~~~i~~~~~LikR 93 (117)
T COG1393 47 LSKLGDGVEELINTRGTTYRELN---LDKEDLSDEELIEALLENPSLIKR 93 (117)
T ss_pred HHHcCccHHHHHHhccchHHHcC---CcccccChHHHHHHHHhChhhccC
Confidence 46789999999999987766655 555566778888899999966653
No 17
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=60.79 E-value=51 Score=31.05 Aligned_cols=70 Identities=21% Similarity=0.140 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcC--------CCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHH
Q 024500 189 KKLFELLVLSGALSELTWPAILSKRHIFREVFVG--------FDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENAR 260 (266)
Q Consensus 189 r~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~--------FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NAr 260 (266)
.-+||.|+--+.+.-+|-..+-+-+.-|.+.|.+ =.|+.|+..+++.+.+ +..++.|.+.|++=|+
T Consensus 103 ~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l~~------~g~s~~Ka~yi~~~A~ 176 (285)
T COG0122 103 PDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALRR------CGLSGRKAEYIISLAR 176 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHHHH------hCCcHHHHHHHHHHHH
Confidence 4589999999999999999988888999999984 5899999999999873 3467899999999999
Q ss_pred HHHh
Q 024500 261 QISK 264 (266)
Q Consensus 261 ailk 264 (266)
++..
T Consensus 177 ~~~~ 180 (285)
T COG0122 177 AAAE 180 (285)
T ss_pred HHHc
Confidence 8763
No 18
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=57.39 E-value=26 Score=24.59 Aligned_cols=43 Identities=23% Similarity=0.288 Sum_probs=32.2
Q ss_pred HHHHHHh-cCC-CHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHH
Q 024500 214 HIFREVF-VGF-DPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (266)
Q Consensus 214 e~FReAF-~~F-Dp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~N 258 (266)
+.|.+.| .++ |-..+..+++++++.+... .+-+|.||...|..
T Consensus 18 ~~y~~~F~~~~i~g~~L~~lt~~dL~~lgi~--~~ghr~ki~~~i~~ 62 (64)
T PF00536_consen 18 EQYAENFEKNYIDGEDLLSLTEEDLEELGIT--KLGHRKKILRAIQK 62 (64)
T ss_dssp GGGHHHHHHTTSSHHHHTTSCHHHHHHTT-S--SHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCchHHHHHhcCHHHHHHcCCC--CHHHHHHHHHHHHH
Confidence 5677777 444 9999999999999996443 24678888877764
No 19
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=50.48 E-value=76 Score=22.91 Aligned_cols=52 Identities=12% Similarity=0.016 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccc
Q 024500 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSA 242 (266)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d 242 (266)
|++.+....-..|+|=.||-.-+..++.-..-|+-..+..++.++|+.-+..
T Consensus 1 Ll~~f~~~l~~~~~s~~Ti~~Y~~~l~~f~~~~~~~~~~~it~~~i~~y~~~ 52 (85)
T PF13495_consen 1 LLEEFLEYLRLKGLSEKTIKNYRYHLKRFLRFLGNKPPDEITPEDIEQYLNY 52 (85)
T ss_dssp -HHHHHHHHHHTT--HHHHHHHHHHHHHHHTTSSS--GGG--HHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcccCccchhHHHHHHHHHHH
Confidence 4455556666799999999999999998777777678899999999876654
No 20
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=49.72 E-value=30 Score=24.35 Aligned_cols=43 Identities=26% Similarity=0.331 Sum_probs=31.2
Q ss_pred HHHHHHhc--CCCH-HHHhcCCHHHHHHhcccchhhcchhHHHHHHHH
Q 024500 214 HIFREVFV--GFDP-IAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (266)
Q Consensus 214 e~FReAF~--~FDp-~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~N 258 (266)
+.|.+.|. +||- +.+..++++++.++.... .-+|.||-..|.+
T Consensus 19 ~~y~~~f~~~~i~g~~~L~~l~~~~L~~lGI~~--~~~r~kll~~i~~ 64 (66)
T PF07647_consen 19 EQYADNFRENGIDGLEDLLQLTEEDLKELGITN--LGHRRKLLSAIQE 64 (66)
T ss_dssp GGGHHHHHHTTCSHHHHHTTSCHHHHHHTTTTH--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHhhCCHHHHHHcCCCC--HHHHHHHHHHHHH
Confidence 56777776 5666 679999999999886643 3567777766654
No 21
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=48.88 E-value=52 Score=29.96 Aligned_cols=67 Identities=13% Similarity=0.097 Sum_probs=47.6
Q ss_pred ChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHH
Q 024500 187 DDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQ 261 (266)
Q Consensus 187 DDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NAra 261 (266)
|+.-+||.|+..+.-+.-+|..+.+--+.+ ++..+ .+++++|+++....+.=-.++|=+-|++-|+.
T Consensus 33 ~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L-------~~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~ 99 (208)
T PRK01229 33 DEEDLFSELSFCILTANSSAEGGIKAQKEI-------GDGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKL 99 (208)
T ss_pred ccCChHHHHHHHHhcCcCcHHHHHHHHHhc-------CHHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHH
Confidence 778899999999999999999988765555 34445 78999999887654211234555555555544
No 22
>PF14493 HTH_40: Helix-turn-helix domain
Probab=36.71 E-value=1.3e+02 Score=22.96 Aligned_cols=46 Identities=15% Similarity=0.036 Sum_probs=32.7
Q ss_pred HHHHHHHhccCcHHHHHHhH-----------HHHHHHhcCCCHHHHhcCCHHHHHHhcc
Q 024500 194 LLVLSGALSELTWPAILSKR-----------HIFREVFVGFDPIAVSKLNEKKLLAAGS 241 (266)
Q Consensus 194 ~L~LEgfQAGLSW~tILkKR-----------e~FReAF~~FDp~kVA~~~E~~Ie~L~~ 241 (266)
..+++.||.|+|-..|-++| ..+-.....||+..+ +++++++.+..
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~~~--l~~e~~~~I~~ 60 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIEEL--LSEEEIKQIED 60 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHHHh--CCHHHHHHHHH
Confidence 36788888888888887777 345566667888877 77777665433
No 23
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=36.65 E-value=2e+02 Score=26.95 Aligned_cols=79 Identities=14% Similarity=0.060 Sum_probs=50.3
Q ss_pred CCCccccChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhc----------CC-CHHHHhcCCHHHHHHhcccchhhcc
Q 024500 180 EWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFV----------GF-DPIAVSKLNEKKLLAAGSAASSLLS 248 (266)
Q Consensus 180 EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~----------~F-Dp~kVA~~~E~~Ie~L~~d~~IIRN 248 (266)
.=|.-+--..-.||.|+-.+.-.-.|=..+.+-..-+-+.|. -| +|+.|+..++++|..+ -..
T Consensus 102 ~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~------Gl~ 175 (283)
T PRK10308 102 RPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKAL------GMP 175 (283)
T ss_pred CCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHC------CCC
Confidence 345555444557998887765555554444444444444433 34 7999999999988753 234
Q ss_pred hhHHHHHHHHHHHHHh
Q 024500 249 ELKLRAIIENARQISK 264 (266)
Q Consensus 249 r~KIrAVI~NArailk 264 (266)
+.|.+.|+.=|+++.+
T Consensus 176 ~~Ra~~L~~lA~~i~~ 191 (283)
T PRK10308 176 LKRAEALIHLANAALE 191 (283)
T ss_pred HHHHHHHHHHHHHHHc
Confidence 6688888888887753
No 24
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=34.83 E-value=1.5e+02 Score=27.59 Aligned_cols=83 Identities=16% Similarity=0.206 Sum_probs=58.7
Q ss_pred hhhhhhhhcCCCccccChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchh
Q 024500 171 PCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSEL 250 (266)
Q Consensus 171 ply~~YHDeEWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~ 250 (266)
.++.-|+|.-|=--...+ |.++=.+.--.-+|..|++.-+.++..+ .+++.+|..+++++++++.-..+--+...
T Consensus 14 ~L~~~yg~q~WWp~~~~~----EiiigAILtQNT~WknvekAlenLk~~~-~~~l~~I~~~~~~~L~elIrpsGFYnqKa 88 (215)
T COG2231 14 ELLRLYGDQGWWPADNKD----EIIIGAILTQNTSWKNVEKALENLKNEG-ILNLKKILKLDEEELAELIRPSGFYNQKA 88 (215)
T ss_pred HHHHHcCCccCCCCCCch----hHHHHHHHhccccHHHHHHHHHHHHHcc-cCCHHHHhcCCHHHHHHHHhccchHHHHH
Confidence 466788888884333332 6554444445678999999999999876 47899999999999999887777655443
Q ss_pred H-HHHHHHH
Q 024500 251 K-LRAIIEN 258 (266)
Q Consensus 251 K-IrAVI~N 258 (266)
| |.|++.|
T Consensus 89 ~rLk~l~k~ 97 (215)
T COG2231 89 KRLKALSKN 97 (215)
T ss_pred HHHHHHHHH
Confidence 2 3344433
No 25
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=33.96 E-value=41 Score=26.72 Aligned_cols=57 Identities=16% Similarity=0.025 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhccCcHHHHHHhHH-HHHHHhcCCCHHHHhcCCHHHH-HHhcccchhhcc
Q 024500 189 KKLFELLVLSGALSELTWPAILSKRH-IFREVFVGFDPIAVSKLNEKKL-LAAGSAASSLLS 248 (266)
Q Consensus 189 r~LFE~L~LEgfQAGLSW~tILkKRe-~FReAF~~FDp~kVA~~~E~~I-e~L~~d~~IIRN 248 (266)
..-++.|.--..+.|..|..++++|. .|++.- .+ +++..++++++ +.|.++|.+|+-
T Consensus 35 ~~~~~el~~~~~~~~~~~~~l~~~~~~~~~~l~--~~-~~~~~~s~~e~~~~l~~~p~LikR 93 (111)
T cd03036 35 PPSKEELKKWLEKSGLPLKKFFNTSGKSYRELG--LK-DKLPSLSEEEALELLSSDGMLIKR 93 (111)
T ss_pred cccHHHHHHHHHHcCCCHHHHHhcCCchHHhCC--cc-cccccCCHHHHHHHHHhCcCeeeC
Confidence 33344454445677888999999996 555552 22 33567776655 567777877763
No 26
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=32.84 E-value=24 Score=24.04 Aligned_cols=27 Identities=11% Similarity=0.202 Sum_probs=16.0
Q ss_pred HHHHhcCCCHHHHhcCCHHHHHHhccc
Q 024500 216 FREVFVGFDPIAVSKLNEKKLLAAGSA 242 (266)
Q Consensus 216 FReAF~~FDp~kVA~~~E~~Ie~L~~d 242 (266)
|+++|.-||.+.=-.++.+++..++..
T Consensus 1 ~~~~F~~~D~~~~G~i~~~el~~~l~~ 27 (67)
T cd00052 1 YDQIFRSLDPDGDGLISGDEARPFLGK 27 (67)
T ss_pred ChHHHHHhCCCCCCcCcHHHHHHHHHH
Confidence 456666676665555566666555433
No 27
>PHA02543 regA translation repressor protein; Provisional
Probab=32.50 E-value=15 Score=31.50 Aligned_cols=59 Identities=19% Similarity=0.219 Sum_probs=44.0
Q ss_pred HHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhH
Q 024500 192 FELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELK 251 (266)
Q Consensus 192 FE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~K 251 (266)
=|||.|.|-|.+|++..|++ |...-+...+++.-.|..-+...-.....+-.+|.++.|
T Consensus 54 KeLl~lDG~~~~~~~eDi~R-rn~Ia~LL~~Wgl~~iv~~~~~~~~~~~n~frVishkqK 112 (125)
T PHA02543 54 KELLALDGRQVDLTEEDIQR-RNNIAKLLEDWGLIEIVDPDQMEEVSPTNNFRVISHKQK 112 (125)
T ss_pred HHHHhhcCcccCCCHHHHHH-HHHHHHHHHhCCceEEeccchhcccCCcCceEEEEeccc
Confidence 37899999999999999986 456667788888777765433222346778888888776
No 28
>PRK01172 ski2-like helicase; Provisional
Probab=32.24 E-value=65 Score=32.99 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=32.7
Q ss_pred CHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHhhC
Q 024500 224 DPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKVW 266 (266)
Q Consensus 224 Dp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~NArailkI~ 266 (266)
++..|+.++++++++++. ....+.+.||+.|+.++.+|
T Consensus 635 ~~~di~~~~~~~~~~i~~-----~~~~~~~~i~~~~~~~~~~~ 672 (674)
T PRK01172 635 TVDDIARSSPERIKKIYG-----FSDTLANAIVNRAMKISSMY 672 (674)
T ss_pred CHHHHHhCCHHHHHHHhc-----cCHHHHHHHHHHHHHHHHHh
Confidence 678888999999988864 56789999999999999875
No 29
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=31.07 E-value=1.6e+02 Score=19.89 Aligned_cols=43 Identities=23% Similarity=0.311 Sum_probs=31.6
Q ss_pred HHHHh--cCCCHHHHhcCC-HHHHHHhcccchhhcchhHHHHHHHHHH
Q 024500 216 FREVF--VGFDPIAVSKLN-EKKLLAAGSAASSLLSELKLRAIIENAR 260 (266)
Q Consensus 216 FReAF--~~FDp~kVA~~~-E~~Ie~L~~d~~IIRNr~KIrAVI~NAr 260 (266)
|.+.| .+||-..+..++ +++++++.... +-+|.||-..|..-+
T Consensus 21 y~~~f~~~~i~g~~ll~~~~~~~l~~lgi~~--~~~r~~ll~~i~~l~ 66 (68)
T smart00454 21 YADNFRKNGIDGALLLLLTSEEDLKELGITK--LGHRKKILKAIQKLK 66 (68)
T ss_pred HHHHHHHCCCCHHHHHhcChHHHHHHcCCCc--HHHHHHHHHHHHHHH
Confidence 66666 577778888998 88888876632 457888887776644
No 30
>PF02173 pKID: pKID domain; InterPro: IPR003102 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB [].; GO: 0005515 protein binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1KDX_B.
Probab=28.94 E-value=17 Score=25.86 Aligned_cols=17 Identities=29% Similarity=0.585 Sum_probs=14.6
Q ss_pred HHHHHhHHHHHHHhcCC
Q 024500 207 PAILSKRHIFREVFVGF 223 (266)
Q Consensus 207 ~tILkKRe~FReAF~~F 223 (266)
..||.+|+.||+.|.+.
T Consensus 13 ReiLsRRPSYRKIlndL 29 (41)
T PF02173_consen 13 REILSRRPSYRKILNDL 29 (41)
T ss_dssp HHHHTTSTHHHHHHHHH
T ss_pred HHHHhhCchHHHHHHHh
Confidence 56999999999998754
No 31
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=27.83 E-value=1.9e+02 Score=28.54 Aligned_cols=76 Identities=22% Similarity=0.174 Sum_probs=56.6
Q ss_pred ChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcC-------------CHHHHHHhcccchhhcchhHHH
Q 024500 187 DDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKL-------------NEKKLLAAGSAASSLLSELKLR 253 (266)
Q Consensus 187 DDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~-------------~E~~Ie~L~~d~~IIRNr~KIr 253 (266)
-|-++|-....+-+-++..|+.++..+ +.|.+|+..++..+ +...+++|.....+|+.+-+..
T Consensus 22 ~~~~~~~~~i~~~~~~~~~~q~~~~~~----~p~l~~~~I~~~~~~~~~~y~~~~~~r~~~~lt~L~s~~~~ll~~v~~~ 97 (328)
T KOG2846|consen 22 SDLYIFTSQIHQLDYAPEKSQSILSQW----QPNLGFPGIILTVRRLSYTYFEYRLNRNTLKLTRLKSQKSKLLELVLET 97 (328)
T ss_pred HHHHHHHHHHHhhhccCchhHHHHHHH----HHHhcchHHHHHHHHHHHhhhheecccchHHHHHHHHHHHHHHHHHHHH
Confidence 344566666677777778888777654 44566666555432 6778999999999999999999
Q ss_pred HHHHHHHHHHhhC
Q 024500 254 AIIENARQISKVW 266 (266)
Q Consensus 254 AVI~NArailkI~ 266 (266)
-...+|..|++.|
T Consensus 98 ~ly~~a~~il~Ry 110 (328)
T KOG2846|consen 98 KLYKVALNILERY 110 (328)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999888653
No 32
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=27.03 E-value=72 Score=28.19 Aligned_cols=32 Identities=22% Similarity=0.387 Sum_probs=28.1
Q ss_pred HHhHHHHHH-HhcCCCHHHHhcCCHHHHHHhcc
Q 024500 210 LSKRHIFRE-VFVGFDPIAVSKLNEKKLLAAGS 241 (266)
Q Consensus 210 LkKRe~FRe-AF~~FDp~kVA~~~E~~Ie~L~~ 241 (266)
++|...||. .|-|+|++.+..|+-+++..|+.
T Consensus 13 ~kKKRTFrkftyrGVdld~Lldms~~~~~~l~~ 45 (152)
T KOG0898|consen 13 LKKKRTFRKFTYRGVDLDQLLDMSTEQLVKLFP 45 (152)
T ss_pred HhhhhhhhhccccCCCHHHHhcCCHHHHHHHHH
Confidence 677777866 68999999999999999988876
No 33
>PF12583 TPPII_N: Tripeptidyl peptidase II N terminal; InterPro: IPR022232 This entry represents a region of approximately 190 amino acids in length and is found in association with PF00082 from PFAM. The members are serine peptidases belonging to MEROPS peptidase family S8A, tripeptidyl peptidase II (TPPII), clan SB. They are a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. ; PDB: 3LXU_X.
Probab=26.92 E-value=36 Score=29.73 Aligned_cols=29 Identities=17% Similarity=0.216 Sum_probs=21.1
Q ss_pred HhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 024500 211 SKRHIFREVFVGFDPIAVSKLNEKKLLAA 239 (266)
Q Consensus 211 kKRe~FReAF~~FDp~kVA~~~E~~Ie~L 239 (266)
.|++.|+|++-+|-+..|++++-+..|.+
T Consensus 70 tk~DeY~EaLRDfq~~~iaKle~e~Ae~v 98 (139)
T PF12583_consen 70 TKWDEYSEALRDFQCSWIAKLEPENAEQV 98 (139)
T ss_dssp --HHHHHHHHHHHHHHHHTTS-HHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHHHhhCHHHHHHH
Confidence 46788999999999999999988655543
No 34
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=25.22 E-value=58 Score=25.15 Aligned_cols=46 Identities=11% Similarity=0.093 Sum_probs=31.8
Q ss_pred HHhccCcHHHHHHhH-HHHHHHhcCCCHHHHhcCCHHHH-HHhcccchhhcc
Q 024500 199 GALSELTWPAILSKR-HIFREVFVGFDPIAVSKLNEKKL-LAAGSAASSLLS 248 (266)
Q Consensus 199 gfQAGLSW~tILkKR-e~FReAF~~FDp~kVA~~~E~~I-e~L~~d~~IIRN 248 (266)
..+.|..+..+++++ ..|++.... ....++++++ +.|.++|.+|+.
T Consensus 45 ~~~~~~~~~~li~~~~~~~~~l~~~----~~~~ls~~e~~~~l~~~p~LikR 92 (105)
T cd02977 45 LAKLGLGVEDLFNTRGTPYRKLGLA----DKDELSDEEALELMAEHPKLIKR 92 (105)
T ss_pred HHhcCCCHHHHHhcCCchHHHcCCc----cccCCCHHHHHHHHHhCcCeeeC
Confidence 356678899999999 667666432 2456776666 557788887764
No 35
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=24.40 E-value=1.3e+02 Score=23.99 Aligned_cols=44 Identities=11% Similarity=0.135 Sum_probs=30.4
Q ss_pred HhccCcHHHHHHhHH-HHHHHhcCCCHHHHhcCCHHH-HHHhcccchhhcc
Q 024500 200 ALSELTWPAILSKRH-IFREVFVGFDPIAVSKLNEKK-LLAAGSAASSLLS 248 (266)
Q Consensus 200 fQAGLSW~tILkKRe-~FReAF~~FDp~kVA~~~E~~-Ie~L~~d~~IIRN 248 (266)
.+.|..+..++++|. .|++.-... ..+++++ ++-|.++|.+|+-
T Consensus 46 ~~~~~~~~~lin~~~~~y~~l~~~~-----~~ls~~e~i~ll~~~P~LikR 91 (112)
T cd03034 46 AKLGISPRDLLRTKEAPYKELGLAD-----PELSDEELIDAMAAHPILIER 91 (112)
T ss_pred HHcCCCHHHHHhcCCchHHHcCCCc-----cCCCHHHHHHHHHhCcCcccC
Confidence 455788999999985 566654332 4778776 5667788887764
No 36
>PF09317 DUF1974: Domain of unknown function (DUF1974); InterPro: IPR015396 This C-terminal domain is functionally uncharacterised and is predominantly found in various prokaryotic acyl-coenzyme a dehydrogenases. ; GO: 0003995 acyl-CoA dehydrogenase activity, 0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase, 0055114 oxidation-reduction process
Probab=24.20 E-value=1e+02 Score=29.41 Aligned_cols=68 Identities=18% Similarity=0.231 Sum_probs=44.0
Q ss_pred hhhhhhhhcCCCccccChHHHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHHHHhcC---------------C---
Q 024500 171 PCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKL---------------N--- 232 (266)
Q Consensus 171 ply~~YHDeEWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~kVA~~---------------~--- 232 (266)
-....|||+ |+|.. |.-|.+.-+-. .+-+-.++|.++|.||..-.++.+ +
T Consensus 114 AvLKr~ed~--Gr~~~-Dlplv~wa~~~---------~l~~~q~Al~~~~~NfP~r~~~~llR~l~fP~G~~~~~PsD~l 181 (284)
T PF09317_consen 114 AVLKRFEDE--GRPEE-DLPLVHWAMQD---------ALYRIQEALDGILRNFPNRALAWLLRALVFPLGRRYRKPSDKL 181 (284)
T ss_pred HHHHHHHhc--CCChh-hHHHHHHHHHH---------HHHHHHHHHHHHHHhCCChHHHHHHHHhhcCCCCCCCCCChHH
Confidence 345678888 98864 44454533222 233445899999999986555422 2
Q ss_pred HHHHHHhcccchhhcchh
Q 024500 233 EKKLLAAGSAASSLLSEL 250 (266)
Q Consensus 233 E~~Ie~L~~d~~IIRNr~ 250 (266)
..+|.++++.++-+|+|.
T Consensus 182 ~~~vA~~l~~p~~~RdRL 199 (284)
T PF09317_consen 182 GHEVARLLMTPGAARDRL 199 (284)
T ss_pred HHHHHHHHcCChHHHHHH
Confidence 245667888888888875
No 37
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=23.95 E-value=55 Score=25.32 Aligned_cols=47 Identities=13% Similarity=0.138 Sum_probs=32.5
Q ss_pred HHHHHHHhcCCC-HHHHh-cCCHHHHHHhccc-----chhhcchhHHHHHHHHH
Q 024500 213 RHIFREVFVGFD-PIAVS-KLNEKKLLAAGSA-----ASSLLSELKLRAIIENA 259 (266)
Q Consensus 213 Re~FReAF~~FD-p~kVA-~~~E~~Ie~L~~d-----~~IIRNr~KIrAVI~NA 259 (266)
-..+++||.-|| .+.=- .++.+++..+|.. -+-.-++..|..++..+
T Consensus 7 ~~~l~~aF~~fD~~dgdG~~I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~ 60 (88)
T cd05027 7 MVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETL 60 (88)
T ss_pred HHHHHHHHHHhcccCCCcCEECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHh
Confidence 356788999997 66655 4888888888876 33334555677777654
No 38
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=23.28 E-value=58 Score=27.10 Aligned_cols=44 Identities=14% Similarity=0.149 Sum_probs=30.1
Q ss_pred HhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHH-HHHhcccchhhc
Q 024500 200 ALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKK-LLAAGSAASSLL 247 (266)
Q Consensus 200 fQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~-Ie~L~~d~~IIR 247 (266)
.+.|+.|..++++|..+.+.. +.+. ..+++++ ++.+++||.+|+
T Consensus 47 ~~~~~~~~~lin~~~~~~k~L-~~~~---~~ls~~e~i~ll~~~P~Lik 91 (132)
T PRK13344 47 TKTENGIESIVSSKNRYAKAL-DCDI---EELSVNEVIDLIQENPRILK 91 (132)
T ss_pred HHhCCCHHHhhccCcHHHHhC-Ccch---hcCCHHHHHHHHHhCcccee
Confidence 456889999999998776543 2332 4566444 566778888776
No 39
>PF12415 rpo132: Poxvirus DNA dependent RNA polymerase; InterPro: IPR024390 All three classes of poxvirus genes - early, intermediate and late - are transcribed by the viral RNA polymerase compex []. This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors. The 132kDa subunit is the second largest subunit of the poxvirus DNA dependent RNA polymerase and shows structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Probab=23.19 E-value=76 Score=21.57 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHh
Q 024500 251 KLRAIIENARQISK 264 (266)
Q Consensus 251 KIrAVI~NArailk 264 (266)
+|.++|+|++.+++
T Consensus 18 lvnalIestk~i~~ 31 (33)
T PF12415_consen 18 LVNALIESTKRILA 31 (33)
T ss_pred HHHHHHHHHHHHHh
Confidence 78999999999875
No 40
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=22.66 E-value=52 Score=25.86 Aligned_cols=45 Identities=9% Similarity=0.123 Sum_probs=30.2
Q ss_pred HhccCcHHHHHHhH-HHHHHHhcCCCHHHHhcCCHHHHHH-hcccchhhcc
Q 024500 200 ALSELTWPAILSKR-HIFREVFVGFDPIAVSKLNEKKLLA-AGSAASSLLS 248 (266)
Q Consensus 200 fQAGLSW~tILkKR-e~FReAF~~FDp~kVA~~~E~~Ie~-L~~d~~IIRN 248 (266)
.+.|..|..+++++ ..|++.. -.....++++++.. |+++|.+|+.
T Consensus 43 ~~~~~~~~~lin~~~~~~k~l~----~~~~~~~s~~e~i~~l~~~p~LikR 89 (110)
T PF03960_consen 43 SKLGNGPDDLINTRSKTYKELG----KLKKDDLSDEELIELLLENPKLIKR 89 (110)
T ss_dssp HHHTSSGGGGB-TTSHHHHHTT----HHHCTTSBHHHHHHHHHHSGGGB-S
T ss_pred HHhcccHHHHhcCccchHhhhh----hhhhhhhhhHHHHHHHHhChhheeC
Confidence 45678899999998 4556554 44557888888754 6677777764
No 41
>PRK10026 arsenate reductase; Provisional
Probab=22.56 E-value=1.3e+02 Score=25.80 Aligned_cols=43 Identities=14% Similarity=0.064 Sum_probs=29.5
Q ss_pred hccCcHHHHHHhH-HHHHHHhcCCCHHHHhcCCHHHH-HHhcccchhhcc
Q 024500 201 LSELTWPAILSKR-HIFREVFVGFDPIAVSKLNEKKL-LAAGSAASSLLS 248 (266)
Q Consensus 201 QAGLSW~tILkKR-e~FReAF~~FDp~kVA~~~E~~I-e~L~~d~~IIRN 248 (266)
+.|+.|..++++| ..|++.-..+ ..++++++ +.|.++|.+|+-
T Consensus 50 ~~g~~~~~lint~~~~yr~L~~~~-----~~ls~~e~l~ll~~~P~LIKR 94 (141)
T PRK10026 50 DMGISVRALLRKNVEPYEELGLAE-----DKFTDDQLIDFMLQHPILINR 94 (141)
T ss_pred hCCCCHHHHHHcCCchHHHcCCCc-----cCCCHHHHHHHHHhCccceeC
Confidence 6799999999999 5667654333 25775554 556677776653
No 42
>PRK04038 rps19p 30S ribosomal protein S19P; Provisional
Probab=22.49 E-value=72 Score=27.67 Aligned_cols=24 Identities=8% Similarity=0.200 Sum_probs=21.5
Q ss_pred HhcCCCHHHHhcCCHHHHHHhccc
Q 024500 219 VFVGFDPIAVSKLNEKKLLAAGSA 242 (266)
Q Consensus 219 AF~~FDp~kVA~~~E~~Ie~L~~d 242 (266)
.|-|+|++.+.+|+.+++..|+..
T Consensus 8 ~yrG~~l~~L~~m~~~~~~~l~~a 31 (134)
T PRK04038 8 TYRGYTLEELQEMSLEEFAELLPA 31 (134)
T ss_pred eecccCHHHHHcCCHHHHHHHcch
Confidence 478999999999999999988765
No 43
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=21.62 E-value=83 Score=25.04 Aligned_cols=56 Identities=16% Similarity=0.057 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHhccCcHHHHHHhHHHHHHHhcCCCHH-HHhcCCHHHH-HHhcccchhhcc
Q 024500 190 KLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPI-AVSKLNEKKL-LAAGSAASSLLS 248 (266)
Q Consensus 190 ~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~~FDp~-kVA~~~E~~I-e~L~~d~~IIRN 248 (266)
.-.+-|.--..+.|..|..++++|... |...... ++..++++++ +-++++|.+|+-
T Consensus 36 ~~~~el~~l~~~~~~~~~~lin~~~~~---~k~l~~~~~~~~ls~~e~~~~i~~~p~LikR 93 (117)
T TIGR01617 36 PTREELLDILSLLEDGIDPLLNTRGQS---YRALNTSNTFLDLSDKEALELLAEDPALLRR 93 (117)
T ss_pred hhHHHHHHHHHHcCCCHHHheeCCCcc---hhhCCchhhcccCCHHHHHHHHHhCcceEec
Confidence 334444444556788999999998654 4444443 3677886665 557777777653
No 44
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=21.26 E-value=1.8e+02 Score=23.06 Aligned_cols=45 Identities=20% Similarity=0.141 Sum_probs=29.1
Q ss_pred HhccCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHH-HHHhcccchhhcc
Q 024500 200 ALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKK-LLAAGSAASSLLS 248 (266)
Q Consensus 200 fQAGLSW~tILkKRe~FReAF~~FDp~kVA~~~E~~-Ie~L~~d~~IIRN 248 (266)
.+.|+.|..++++|...-+.. +.+. ..+++++ |+-++++|.+|+-
T Consensus 47 ~~~~~~~~~l~n~~~~~~k~l-~~~~---~~ls~~e~i~~l~~~p~LikR 92 (115)
T cd03032 47 SLTENGVEDIISTRSKAFKNL-NIDI---DELSLSELIRLISEHPSLLRR 92 (115)
T ss_pred HHhcCCHHHHHhcCcHHHHHc-CCCc---ccCCHHHHHHHHHhChhheeC
Confidence 445778999999997654432 2222 4567555 4567788887764
No 45
>PF14534 DUF4440: Domain of unknown function (DUF4440); PDB: 3HX8_A 3SOY_A 3ROB_B 3GZR_A 3B7C_A 3CU3_A 3FSD_A 2R4I_C 1TP6_A.
Probab=20.62 E-value=95 Score=22.21 Aligned_cols=48 Identities=17% Similarity=0.252 Sum_probs=30.6
Q ss_pred HHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHH
Q 024500 209 ILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIE 257 (266)
Q Consensus 209 ILkKRe~FReAF~~FDp~kVA~~~E~~Ie~L~~d~~IIRNr~KIrAVI~ 257 (266)
|+...+.|.+||...|++.++.+=.++..-... .+-+.++..+-+.+.
T Consensus 1 I~a~~~~~~~A~~~~D~~~~~~~~~~d~~~~~~-~g~~~~~~~~l~~~~ 48 (107)
T PF14534_consen 1 IRALEEQYEDAFNAGDIDALASLYADDFVFVGP-GGTILGKEAILAAFK 48 (107)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHTTEEEEEEEEET-TSEEEEHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCHHHHHhhhCCCEEEECC-CCCEeCHHHHHHHHh
Confidence 677788999999999999998774444332222 233345555544443
No 46
>PF05075 DUF684: Protein of unknown function (DUF684); InterPro: IPR007767 This family contains uncharacterised proteins from Caenorhabditis elegans.
Probab=20.56 E-value=1.9e+02 Score=27.83 Aligned_cols=40 Identities=23% Similarity=0.124 Sum_probs=29.8
Q ss_pred hHHHHHHHHHHHHhccC-------cHHHHHHhHHHHHHHhcCCCHHH
Q 024500 188 DKKLFELLVLSGALSEL-------TWPAILSKRHIFREVFVGFDPIA 227 (266)
Q Consensus 188 Dr~LFE~L~LEgfQAGL-------SW~tILkKRe~FReAF~~FDp~k 227 (266)
+..|-.+|.||+|.+|| .+..|+.+-..+.+..+.|+-+-
T Consensus 115 ~~vl~q~l~lEafa~Gl~~~~n~~~~~~L~e~~~~~~~~~~~w~~~Y 161 (345)
T PF05075_consen 115 DGVLGQLLFLEAFASGLFKDKNMYDPDRLIEKIEEINEKMDKWKEEY 161 (345)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 35688999999999999 56778877777666666555443
Done!