Query 024277
Match_columns 270
No_of_seqs 194 out of 1145
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:23:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024277.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024277hhsearch_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 1E-51 2.3E-56 361.7 11.6 107 160-268 2-108 (187)
2 TIGR00624 tag DNA-3-methyladen 100.0 2.3E-51 5.1E-56 357.3 11.6 107 160-268 1-107 (179)
3 COG2818 Tag 3-methyladenine DN 100.0 9.5E-50 2.1E-54 349.7 10.8 109 159-268 1-109 (188)
4 PF03352 Adenine_glyco: Methyl 100.0 4.9E-48 1.1E-52 336.3 9.5 103 164-268 1-103 (179)
5 cd00056 ENDO3c endonuclease II 94.0 0.32 7E-06 40.0 7.9 70 192-265 1-70 (158)
6 PF00730 HhH-GPD: HhH-GPD supe 91.3 1.3 2.7E-05 34.3 7.5 63 199-263 4-66 (108)
7 PRK10702 endonuclease III; Pro 91.2 1.7 3.7E-05 39.0 9.1 70 191-264 29-98 (211)
8 TIGR01083 nth endonuclease III 89.7 2.6 5.5E-05 36.7 8.7 70 191-264 26-95 (191)
9 TIGR03252 uncharacterized HhH- 88.2 4.1 8.8E-05 36.5 9.0 73 191-264 18-93 (177)
10 PRK13913 3-methyladenine DNA g 87.2 5 0.00011 36.7 9.2 72 191-264 30-106 (218)
11 smart00478 ENDO3c endonuclease 85.2 3.5 7.5E-05 33.7 6.5 57 204-264 5-61 (149)
12 PRK10880 adenine DNA glycosyla 82.7 8.7 0.00019 37.4 9.1 69 191-264 30-98 (350)
13 TIGR01084 mutY A/G-specific ad 78.7 11 0.00023 35.4 8.0 69 191-264 26-94 (275)
14 COG0177 Nth Predicted EndoIII- 69.2 31 0.00068 31.7 8.4 69 191-264 29-98 (211)
15 cd00166 SAM Sterile alpha moti 68.8 13 0.00028 25.3 4.6 43 214-258 17-61 (63)
16 COG1393 ArsC Arsenate reductas 66.5 6.7 0.00015 32.4 3.2 47 198-247 46-92 (117)
17 COG0122 AlkA 3-methyladenine D 62.1 44 0.00096 31.5 8.2 71 189-265 103-181 (285)
18 PF00536 SAM_1: SAM domain (St 56.5 26 0.00057 24.7 4.4 43 214-258 18-62 (64)
19 PRK01229 N-glycosylase/DNA lya 54.6 40 0.00088 30.7 6.3 67 187-261 33-99 (208)
20 PF07647 SAM_2: SAM domain (St 48.7 31 0.00068 24.3 3.8 43 214-258 19-64 (66)
21 PF13495 Phage_int_SAM_4: Phag 46.9 1.1E+02 0.0024 22.1 7.1 52 191-242 1-52 (85)
22 COG2231 Uncharacterized protei 38.1 1.3E+02 0.0027 28.2 6.8 83 171-258 14-97 (215)
23 PHA02543 regA translation repr 35.3 14 0.0003 31.8 0.3 59 192-251 54-112 (125)
24 PF14493 HTH_40: Helix-turn-he 35.0 1.6E+02 0.0034 22.6 6.1 46 194-241 4-60 (91)
25 cd03036 ArsC_like Arsenate Red 33.6 45 0.00097 26.6 2.9 57 188-247 34-92 (111)
26 cd00052 EH Eps15 homology doma 33.2 26 0.00057 23.9 1.3 27 216-242 1-27 (67)
27 smart00454 SAM Sterile alpha m 32.4 1.4E+02 0.003 20.2 4.9 43 216-260 21-66 (68)
28 PRK10308 3-methyl-adenine DNA 30.7 2.7E+02 0.0058 26.2 7.9 79 180-264 102-191 (283)
29 KOG4384 Uncharacterized SAM do 30.5 55 0.0012 32.6 3.5 46 219-266 235-281 (361)
30 KOG0898 40S ribosomal protein 27.5 70 0.0015 28.4 3.2 32 210-241 13-45 (152)
31 cd05027 S-100B S-100B: S-100B 26.0 53 0.0011 25.5 2.1 47 213-259 7-60 (88)
32 PRK13344 spxA transcriptional 24.8 57 0.0012 27.2 2.2 44 200-247 47-91 (132)
33 PF12583 TPPII_N: Tripeptidyl 24.7 42 0.00091 29.4 1.4 29 211-239 70-98 (139)
34 PF12415 rpo132: Poxvirus DNA 23.9 74 0.0016 21.7 2.2 14 251-264 18-31 (33)
35 PF09317 DUF1974: Domain of un 22.4 1.1E+02 0.0024 29.2 3.9 68 171-250 114-199 (284)
36 cd03032 ArsC_Spx Arsenate Redu 21.9 1.8E+02 0.0039 23.1 4.5 45 200-248 47-92 (115)
37 PF02173 pKID: pKID domain; I 21.6 28 0.0006 24.8 -0.2 17 207-223 13-29 (41)
38 PF03960 ArsC: ArsC family; I 21.0 66 0.0014 25.3 1.8 44 200-247 43-88 (110)
39 TIGR01617 arsC_related transcr 20.7 90 0.0019 24.9 2.5 54 191-247 37-92 (117)
40 PRK04038 rps19p 30S ribosomal 20.4 85 0.0018 27.3 2.4 24 219-242 8-31 (134)
41 PF14534 DUF4440: Domain of un 20.0 98 0.0021 22.2 2.4 48 209-257 1-48 (107)
No 1
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=100.00 E-value=1e-51 Score=361.68 Aligned_cols=107 Identities=40% Similarity=0.758 Sum_probs=104.9
Q ss_pred CCCCCCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 024277 160 KRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAA 239 (270)
Q Consensus 160 ~RC~Wat~~sdply~~YHD~EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~L 239 (270)
.||.|++ +||+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||++|||++||+|+|++|++|
T Consensus 2 ~rC~W~~--~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~L 79 (187)
T PRK10353 2 ERCGWVS--QDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERL 79 (187)
T ss_pred CCCCCCC--CChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHH
Confidence 6999996 79999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhhcchhHHHHHHHHHHHHHHhccc
Q 024277 240 GSAASSLLSELKLRAIIENARQISKVGYP 268 (270)
Q Consensus 240 l~d~~IIRNr~KI~AVI~NArailkI~~~ 268 (270)
|+|++|||||+||+|||+||+++++|+++
T Consensus 80 l~d~~IIRnr~KI~Avi~NA~~~l~i~~e 108 (187)
T PRK10353 80 VQDAGIIRHRGKIQAIIGNARAYLQMEQN 108 (187)
T ss_pred hcCchhHHhHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999875
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=2.3e-51 Score=357.29 Aligned_cols=107 Identities=35% Similarity=0.675 Sum_probs=104.3
Q ss_pred CCCCCCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 024277 160 KRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAA 239 (270)
Q Consensus 160 ~RC~Wat~~sdply~~YHD~EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~L 239 (270)
.||.|++ ++|+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||+||||++||.|+|++|++|
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 cccchhhcchhHHHHHHHHHHHHHHhccc
Q 024277 240 GSAASSLLSELKLRAIIENARQISKVGYP 268 (270)
Q Consensus 240 l~d~~IIRNr~KI~AVI~NArailkI~~~ 268 (270)
|+|++|||||+||+|||+||+++++|+++
T Consensus 79 ~~d~~IIRnr~KI~Avi~NA~~~l~i~~e 107 (179)
T TIGR00624 79 LQDDGIIRNRGKIEATIANARAALQLEQN 107 (179)
T ss_pred hcCccchhhHHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999999999764
No 3
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.5e-50 Score=349.71 Aligned_cols=109 Identities=43% Similarity=0.794 Sum_probs=105.4
Q ss_pred CCCCCCCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 024277 159 KKRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLA 238 (270)
Q Consensus 159 ~~RC~Wat~~sdply~~YHD~EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~ 238 (270)
+.||.|+. +.+|+|.+|||+|||+|++||+.|||+||||+|||||||.|||+||++||+||++|||++||.|+|++|++
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 36999996 34899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccchhhcchhHHHHHHHHHHHHHHhccc
Q 024277 239 AGSAASSLLSELKLRAIIENARQISKVGYP 268 (270)
Q Consensus 239 Ll~d~~IIRNr~KI~AVI~NArailkI~~~ 268 (270)
||+|++|||||+||.|||+|||++++|+++
T Consensus 80 Ll~d~gIIR~r~KI~A~i~NA~~~l~l~~e 109 (188)
T COG2818 80 LLADAGIIRNRGKIKATINNARAVLELQKE 109 (188)
T ss_pred HHhCcchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999876
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=4.9e-48 Score=336.35 Aligned_cols=103 Identities=48% Similarity=0.867 Sum_probs=92.9
Q ss_pred CCCCCCChhhhhhhhcCCCccccChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccc
Q 024277 164 WVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAA 243 (270)
Q Consensus 164 Wat~~sdply~~YHD~EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~ 243 (270)
|+. ++|+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||+||||++||+|+|++|++||+|+
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 789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcchhHHHHHHHHHHHHHHhccc
Q 024277 244 SSLLSELKLRAIIENARQISKVGYP 268 (270)
Q Consensus 244 ~IIRNr~KI~AVI~NArailkI~~~ 268 (270)
+|||||+||+|||+||+++++|+++
T Consensus 79 ~iIRnr~KI~Avi~NA~~~l~i~~e 103 (179)
T PF03352_consen 79 GIIRNRRKIRAVINNARAILKIQEE 103 (179)
T ss_dssp TSS--HHHHHHHHHHHHHHHHHHHT
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999875
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=94.04 E-value=0.32 Score=40.03 Aligned_cols=70 Identities=23% Similarity=0.122 Sum_probs=59.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHHh
Q 024277 192 FELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKV 265 (270)
Q Consensus 192 FE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailkI 265 (270)
||.|+-.++..-.+|..+.+-...|.+.|. .+++.|+..++++|..+...-+ .+.|.+.|++=|+.+.+-
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g-pt~~~l~~~~~~~l~~~~~~~G---~~~kA~~i~~~a~~~~~~ 70 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG-PTPEALAAADEEELRELIRSLG---YRRKAKYLKELARAIVEG 70 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC-CCHHHHHCCCHHHHHHHHHhcC---hHHHHHHHHHHHHHHHHH
Confidence 688888888888999999998888888875 7999999999999998766544 478999999888888763
No 6
>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=91.33 E-value=1.3 Score=34.27 Aligned_cols=63 Identities=22% Similarity=0.045 Sum_probs=52.2
Q ss_pred HHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHH
Q 024277 199 GALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQIS 263 (270)
Q Consensus 199 gfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArail 263 (270)
++..-.+|..+.+-...|.+.|...+++.|+..++++|.++... .--++.|-+.|++=|+.++
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 44556789999999999999999999999999999999998665 3356678888988888875
No 7
>PRK10702 endonuclease III; Provisional
Probab=91.17 E-value=1.7 Score=39.04 Aligned_cols=70 Identities=17% Similarity=0.095 Sum_probs=54.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHH
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailk 264 (270)
-||.|+-++.-+--+|..|.+--+.|.+.| .+++.+++.++++|+.+...-|. .+.|-..+++.|+.+++
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 599999999988999999987777666544 48999999999999987665443 34566677888887765
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=89.69 E-value=2.6 Score=36.71 Aligned_cols=70 Identities=21% Similarity=0.157 Sum_probs=55.4
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHH
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailk 264 (270)
-||.|+-++.-.-.+|..+.+--..|.+.| .+++.|+..++++|++++.--+. .+.|.+.|++=|+.+++
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 45677777777777654
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=88.22 E-value=4.1 Score=36.49 Aligned_cols=73 Identities=14% Similarity=0.081 Sum_probs=54.3
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHH-HHHhcCCCHHHHhcCCHHHHHHhccc-chhhc-chhHHHHHHHHHHHHHH
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIF-REVFVGFDPIAVSKLNEKKLLAAGSA-ASSLL-SELKLRAIIENARQISK 264 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~F-ReAF~gFDp~kVA~~~E~~Ie~Ll~d-~~IIR-Nr~KI~AVI~NArailk 264 (270)
-||+|+--+.-+--+|..+.+--+.+ +++|. .||+.|+.++.++|++++.. +++.+ .+.|=+-|++=|+.|++
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 49999999999999999988666555 44554 89999999999999988753 33222 34666666666666653
No 10
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=87.19 E-value=5 Score=36.65 Aligned_cols=72 Identities=15% Similarity=0.200 Sum_probs=55.3
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhc-----CCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHH
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFV-----GFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~-----gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailk 264 (270)
-||.|+-.+.-.--+|..+.+-=+.+++.|. .-+++.|+.+++++|+++....| -.++|.+.+.+=|+.+++
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 456777778777777754
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=85.15 E-value=3.5 Score=33.71 Aligned_cols=57 Identities=19% Similarity=0.152 Sum_probs=46.2
Q ss_pred CCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHH
Q 024277 204 LTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (270)
Q Consensus 204 LSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailk 264 (270)
.+|..+.+--..|.+.|- +|+.|+..++++|.+++..-+ ..+.|.+.|++.|+.+.+
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 577888888888888876 799999999999988765522 456799999999988765
No 12
>PRK10880 adenine DNA glycosylase; Provisional
Probab=82.72 E-value=8.7 Score=37.36 Aligned_cols=69 Identities=10% Similarity=0.121 Sum_probs=56.2
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHH
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailk 264 (270)
-|+.|+-|++..--+|.+++.--+.|.+.| .|++.+|..++++|..+..--|.- + |.+-+.+-|+.+.+
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--A-RARNLHKAAQQVAT 98 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHC--cCHHHHHCcCHHHHHHHHHcCChH--H-HHHHHHHHHHHHHH
Confidence 489999999999999999999888888876 579999999999999877665653 2 66667777776643
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=78.71 E-value=11 Score=35.41 Aligned_cols=69 Identities=12% Similarity=0.141 Sum_probs=55.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHH
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailk 264 (270)
.|+.|+-+++..-.+|.+++.-.+.|.+.| -+++.+|..++++|..+...-+.- .|.+.+.+=|+.|.+
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 699999999999999999999998898887 579999999999998876655553 245666666666644
No 14
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=69.19 E-value=31 Score=31.66 Aligned_cols=69 Identities=23% Similarity=0.182 Sum_probs=47.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCC-HHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHH
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFD-PIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFD-p~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailk 264 (270)
-||+|+--+.-+-=+=..+- .++++.|.-|+ |+.++..++++|+.+...-+ ..|.|-..|+.=|+.+++
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 58877644333322222221 45666777776 99999999999999988655 455666778888888875
No 15
>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=68.84 E-value=13 Score=25.32 Aligned_cols=43 Identities=21% Similarity=0.196 Sum_probs=32.3
Q ss_pred HHHHHHh--cCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHH
Q 024277 214 HIFREVF--VGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (270)
Q Consensus 214 e~FReAF--~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~N 258 (270)
+.|.+.| .+||-..+..++++++..+.... .-+|.||...|.+
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 5677777 57899999999999999765532 4577888766654
No 16
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=66.48 E-value=6.7 Score=32.41 Aligned_cols=47 Identities=9% Similarity=-0.168 Sum_probs=36.3
Q ss_pred HHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhc
Q 024277 198 SGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLL 247 (270)
Q Consensus 198 EgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIR 247 (270)
-..+.|..|..+++++..+-+... .++....+++.++.++.++.+|+
T Consensus 46 ~l~~~g~~~~~li~t~~~~~r~L~---~~~~~~~~~~~~~~i~~~~~Lik 92 (117)
T COG1393 46 ILSKLGDGVEELINTRGTTYRELN---LDKEDLSDEELIEALLENPSLIK 92 (117)
T ss_pred HHHHcCccHHHHHHhccchHHHcC---CcccccChHHHHHHHHhChhhcc
Confidence 346889999999999988766665 55556677888888999986655
No 17
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=62.10 E-value=44 Score=31.51 Aligned_cols=71 Identities=21% Similarity=0.122 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcC--------CCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHH
Q 024277 189 KKLFELLVLSGALSELTWPAILSKRHIFREVFVG--------FDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENAR 260 (270)
Q Consensus 189 r~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~g--------FDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NAr 260 (270)
.-+||.|+--+.+.-+|-..+-+-+.-|.+.|.+ =.|+.|+..+++.+.+ +..++.|.+.|++=|+
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 4589999999999999999998889999999984 5899999999999874 3467899999999999
Q ss_pred HHHHh
Q 024277 261 QISKV 265 (270)
Q Consensus 261 ailkI 265 (270)
++..-
T Consensus 177 ~~~~g 181 (285)
T COG0122 177 AAAEG 181 (285)
T ss_pred HHHcC
Confidence 88653
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=56.48 E-value=26 Score=24.66 Aligned_cols=43 Identities=23% Similarity=0.288 Sum_probs=31.8
Q ss_pred HHHHHHh-cCC-CHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHH
Q 024277 214 HIFREVF-VGF-DPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (270)
Q Consensus 214 e~FReAF-~gF-Dp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~N 258 (270)
+.|.+.| .++ |-..+..+++++++.+... .+-+|.||...|..
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 9999999999999995443 24588888877764
No 19
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=54.63 E-value=40 Score=30.69 Aligned_cols=67 Identities=13% Similarity=0.097 Sum_probs=48.3
Q ss_pred ChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHH
Q 024277 187 DDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQ 261 (270)
Q Consensus 187 DDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NAra 261 (270)
|+.-+||.|+..+.-+.-+|..+.+--+.+ +++.+ .+++++|++++...+.=-.++|=+-|++-++.
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 788899999999999999999988765555 34445 78999999887654311335555556555554
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=48.72 E-value=31 Score=24.33 Aligned_cols=43 Identities=26% Similarity=0.331 Sum_probs=30.9
Q ss_pred HHHHHHhc--CCCH-HHHhcCCHHHHHHhcccchhhcchhHHHHHHHH
Q 024277 214 HIFREVFV--GFDP-IAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (270)
Q Consensus 214 e~FReAF~--gFDp-~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~N 258 (270)
+.|.+.|. +||- +.+..++++++.++.... .-+|.||...|++
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 45667776 6666 779999999999886632 3567777766654
No 21
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=46.85 E-value=1.1e+02 Score=22.13 Aligned_cols=52 Identities=12% Similarity=0.016 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccc
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSA 242 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d 242 (270)
|++.+....-..|+|=.||-.-+..++.-..-|+-..+..++.++|+..+..
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 4455555666699999999999999998888887678999999999986654
No 22
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=38.08 E-value=1.3e+02 Score=28.23 Aligned_cols=83 Identities=16% Similarity=0.237 Sum_probs=58.7
Q ss_pred hhhhhhhhcCCCccccChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchh
Q 024277 171 PCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSEL 250 (270)
Q Consensus 171 ply~~YHD~EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~ 250 (270)
.++..|+|.-|=--...+ |.++=.+.--.-+|..|.+.-+.++..+. +|+.+|..+++++++.+....|--+...
T Consensus 14 ~L~~~yg~q~WWp~~~~~----EiiigAILtQNT~WknvekAlenLk~~~~-~~l~~I~~~~~~~L~elIrpsGFYnqKa 88 (215)
T COG2231 14 ELLRLYGDQGWWPADNKD----EIIIGAILTQNTSWKNVEKALENLKNEGI-LNLKKILKLDEEELAELIRPSGFYNQKA 88 (215)
T ss_pred HHHHHcCCccCCCCCCch----hHHHHHHHhccccHHHHHHHHHHHHHccc-CCHHHHhcCCHHHHHHHHhccchHHHHH
Confidence 467789998884332222 65544444556789999999999998764 6799999999999999887776655443
Q ss_pred H-HHHHHHH
Q 024277 251 K-LRAIIEN 258 (270)
Q Consensus 251 K-I~AVI~N 258 (270)
| |.|++.|
T Consensus 89 ~rLk~l~k~ 97 (215)
T COG2231 89 KRLKALSKN 97 (215)
T ss_pred HHHHHHHHH
Confidence 2 3344443
No 23
>PHA02543 regA translation repressor protein; Provisional
Probab=35.29 E-value=14 Score=31.75 Aligned_cols=59 Identities=19% Similarity=0.219 Sum_probs=44.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhH
Q 024277 192 FELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELK 251 (270)
Q Consensus 192 FE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~K 251 (270)
=|||.|.|-|.+|++..|++ |...-+...+++.-.|..=+.-+-.....+-++|.++.|
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 556667778888777765433222346778888888876
No 24
>PF14493 HTH_40: Helix-turn-helix domain
Probab=35.02 E-value=1.6e+02 Score=22.63 Aligned_cols=46 Identities=15% Similarity=0.036 Sum_probs=32.2
Q ss_pred HHHHHHHhcCCCHHHHHHhH-----------HHHHHHhcCCCHHHHhcCCHHHHHHhcc
Q 024277 194 LLVLSGALSELTWPAILSKR-----------HIFREVFVGFDPIAVSKLNEKKLLAAGS 241 (270)
Q Consensus 194 ~L~LEgfQAGLSW~tILkKR-----------e~FReAF~gFDp~kVA~~~E~~Ie~Ll~ 241 (270)
..+++-||.|+|-..|-++| ..+-+.+..||+..+ +++++++.+..
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 36778888888888777777 345566666888877 77777665443
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=33.64 E-value=45 Score=26.59 Aligned_cols=57 Identities=16% Similarity=0.042 Sum_probs=36.0
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHHhHH-HHHHHhcCCCHHHHhcCCHHHH-HHhcccchhhc
Q 024277 188 DKKLFELLVLSGALSELTWPAILSKRH-IFREVFVGFDPIAVSKLNEKKL-LAAGSAASSLL 247 (270)
Q Consensus 188 Dr~LFE~L~LEgfQAGLSW~tILkKRe-~FReAF~gFDp~kVA~~~E~~I-e~Ll~d~~IIR 247 (270)
|..-++.|.--..+.|..|..++++|. .|++.- .+ +++..++++++ +.|.++|.+|+
T Consensus 34 ~~~~~~el~~~~~~~~~~~~~l~~~~~~~~~~l~--~~-~~~~~~s~~e~~~~l~~~p~Lik 92 (111)
T cd03036 34 EPPSKEELKKWLEKSGLPLKKFFNTSGKSYRELG--LK-DKLPSLSEEEALELLSSDGMLIK 92 (111)
T ss_pred CcccHHHHHHHHHHcCCCHHHHHhcCCchHHhCC--cc-cccccCCHHHHHHHHHhCcCeee
Confidence 333344454445677889999999997 555542 22 34567776655 55666777765
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=33.18 E-value=26 Score=23.94 Aligned_cols=27 Identities=11% Similarity=0.202 Sum_probs=16.8
Q ss_pred HHHHhcCCCHHHHhcCCHHHHHHhccc
Q 024277 216 FREVFVGFDPIAVSKLNEKKLLAAGSA 242 (270)
Q Consensus 216 FReAF~gFDp~kVA~~~E~~Ie~Ll~d 242 (270)
|+++|.-||.+.=-.++.+++..++..
T Consensus 1 ~~~~F~~~D~~~~G~i~~~el~~~l~~ 27 (67)
T cd00052 1 YDQIFRSLDPDGDGLISGDEARPFLGK 27 (67)
T ss_pred ChHHHHHhCCCCCCcCcHHHHHHHHHH
Confidence 466777777666556666666655543
No 27
>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=32.42 E-value=1.4e+02 Score=20.22 Aligned_cols=43 Identities=23% Similarity=0.311 Sum_probs=31.1
Q ss_pred HHHHh--cCCCHHHHhcCC-HHHHHHhcccchhhcchhHHHHHHHHHH
Q 024277 216 FREVF--VGFDPIAVSKLN-EKKLLAAGSAASSLLSELKLRAIIENAR 260 (270)
Q Consensus 216 FReAF--~gFDp~kVA~~~-E~~Ie~Ll~d~~IIRNr~KI~AVI~NAr 260 (270)
|.+.| .+||-..+..++ +++++++.... +-+|.||...|.+-+
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 677888888998 88888876622 357888877776643
No 28
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=30.67 E-value=2.7e+02 Score=26.20 Aligned_cols=79 Identities=14% Similarity=0.060 Sum_probs=50.7
Q ss_pred CCCccccChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhc----------CC-CHHHHhcCCHHHHHHhcccchhhcc
Q 024277 180 EWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFV----------GF-DPIAVSKLNEKKLLAAGSAASSLLS 248 (270)
Q Consensus 180 EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~----------gF-Dp~kVA~~~E~~Ie~Ll~d~~IIRN 248 (270)
.=|.-+.-..-.||+|+-.+.-.-.|=..+.+-..-|-+.|. -| +|+.|+..++++|..+ =..
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 335555444567999887765444454444443444444433 34 7999999999988753 235
Q ss_pred hhHHHHHHHHHHHHHH
Q 024277 249 ELKLRAIIENARQISK 264 (270)
Q Consensus 249 r~KI~AVI~NArailk 264 (270)
+.|.+.|+.=|+++.+
T Consensus 176 ~~Ra~~L~~lA~~i~~ 191 (283)
T PRK10308 176 LKRAEALIHLANAALE 191 (283)
T ss_pred HHHHHHHHHHHHHHHc
Confidence 6788888888888765
No 29
>KOG4384 consensus Uncharacterized SAM domain protein [General function prediction only]
Probab=30.50 E-value=55 Score=32.64 Aligned_cols=46 Identities=20% Similarity=0.203 Sum_probs=36.6
Q ss_pred HhcCCC-HHHHhcCCHHHHHHhcccchhhcchhHHHHHHHHHHHHHHhc
Q 024277 219 VFVGFD-PIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKVG 266 (270)
Q Consensus 219 AF~gFD-p~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~NArailkI~ 266 (270)
.+.||| ++.+..++|+|++.|..+. --||+||...|++-+-+-...
T Consensus 235 L~nGYd~le~~k~i~e~dL~~lgI~n--P~Hr~kLL~av~~~~e~d~~~ 281 (361)
T KOG4384|consen 235 LENGYDTLEDLKDITEEDLEELGIDN--PDHRKKLLSAVELLKEIDSGS 281 (361)
T ss_pred HHcchHHHHHHHhccHHHHHHhCCCC--HHHHHHHHHHHHHHHhccccc
Confidence 457898 9999999999999987632 258999999998877665443
No 30
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=27.48 E-value=70 Score=28.35 Aligned_cols=32 Identities=22% Similarity=0.387 Sum_probs=28.4
Q ss_pred HHhHHHHHH-HhcCCCHHHHhcCCHHHHHHhcc
Q 024277 210 LSKRHIFRE-VFVGFDPIAVSKLNEKKLLAAGS 241 (270)
Q Consensus 210 LkKRe~FRe-AF~gFDp~kVA~~~E~~Ie~Ll~ 241 (270)
++|...||+ .|-|+|++.+..|+-+++..|+.
T Consensus 13 ~kKKRTFrkftyrGVdld~Lldms~~~~~~l~~ 45 (152)
T KOG0898|consen 13 LKKKRTFRKFTYRGVDLDQLLDMSTEQLVKLFP 45 (152)
T ss_pred HhhhhhhhhccccCCCHHHHhcCCHHHHHHHHH
Confidence 777788876 69999999999999999998877
No 31
>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=25.98 E-value=53 Score=25.46 Aligned_cols=47 Identities=13% Similarity=0.138 Sum_probs=32.3
Q ss_pred HHHHHHHhcCCC-HHHHh-cCCHHHHHHhccc-----chhhcchhHHHHHHHHH
Q 024277 213 RHIFREVFVGFD-PIAVS-KLNEKKLLAAGSA-----ASSLLSELKLRAIIENA 259 (270)
Q Consensus 213 Re~FReAF~gFD-p~kVA-~~~E~~Ie~Ll~d-----~~IIRNr~KI~AVI~NA 259 (270)
-..++++|.-|| .+.=- .++.+++..+|.. -+-.-++..|..++..+
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 33333555577777644
No 32
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=24.81 E-value=57 Score=27.17 Aligned_cols=44 Identities=14% Similarity=0.149 Sum_probs=30.0
Q ss_pred HhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHH-HHHhcccchhhc
Q 024277 200 ALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKK-LLAAGSAASSLL 247 (270)
Q Consensus 200 fQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~-Ie~Ll~d~~IIR 247 (270)
.+.|+.|..++++|..+.+.. +.+. ..+++++ ++-++.+|.+|+
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 4566554 556777777776
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=24.70 E-value=42 Score=29.41 Aligned_cols=29 Identities=17% Similarity=0.216 Sum_probs=21.0
Q ss_pred HhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 024277 211 SKRHIFREVFVGFDPIAVSKLNEKKLLAA 239 (270)
Q Consensus 211 kKRe~FReAF~gFDp~kVA~~~E~~Ie~L 239 (270)
.|++.|+|++-+|-+..|++++-+..|.+
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 57788899999999999999988655543
No 34
>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=23.85 E-value=74 Score=21.68 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHH
Q 024277 251 KLRAIIENARQISK 264 (270)
Q Consensus 251 KI~AVI~NArailk 264 (270)
+|.++|+|++.+++
T Consensus 18 lvnalIestk~i~~ 31 (33)
T PF12415_consen 18 LVNALIESTKRILA 31 (33)
T ss_pred HHHHHHHHHHHHHh
Confidence 78999999999875
No 35
>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=22.38 E-value=1.1e+02 Score=29.23 Aligned_cols=68 Identities=18% Similarity=0.231 Sum_probs=43.7
Q ss_pred hhhhhhhhcCCCccccChHHHHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcC---------------C---
Q 024277 171 PCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKL---------------N--- 232 (270)
Q Consensus 171 ply~~YHD~EWG~PvhDDr~LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~kVA~~---------------~--- 232 (270)
.....|||+ |+|.. |.-|.+.-+-. .+-+-.++|.++|.||..-.++-+ +
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 344678888 98864 44454533222 233445889999999986544422 2
Q ss_pred HHHHHHhcccchhhcchh
Q 024277 233 EKKLLAAGSAASSLLSEL 250 (270)
Q Consensus 233 E~~Ie~Ll~d~~IIRNr~ 250 (270)
..+|.++|..++-+|+|.
T Consensus 182 ~~~vA~~l~~p~~~RdRL 199 (284)
T PF09317_consen 182 GHEVARLLMTPGAARDRL 199 (284)
T ss_pred HHHHHHHHcCChHHHHHH
Confidence 245677888888888874
No 36
>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=21.93 E-value=1.8e+02 Score=23.15 Aligned_cols=45 Identities=22% Similarity=0.149 Sum_probs=28.9
Q ss_pred HhcCCCHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHH-HHhcccchhhcc
Q 024277 200 ALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKL-LAAGSAASSLLS 248 (270)
Q Consensus 200 fQAGLSW~tILkKRe~FReAF~gFDp~kVA~~~E~~I-e~Ll~d~~IIRN 248 (270)
.+.|+.|..++++|...-+.. +.+. ..++++++ +-++++|.+|+-
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 445788999999997654432 2222 45676654 556677777663
No 37
>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=21.61 E-value=28 Score=24.82 Aligned_cols=17 Identities=29% Similarity=0.585 Sum_probs=14.5
Q ss_pred HHHHHhHHHHHHHhcCC
Q 024277 207 PAILSKRHIFREVFVGF 223 (270)
Q Consensus 207 ~tILkKRe~FReAF~gF 223 (270)
..||.+|+.||+.|.+.
T Consensus 13 ReiLsRRPSYRKIlndL 29 (41)
T PF02173_consen 13 REILSRRPSYRKILNDL 29 (41)
T ss_dssp HHHHTTSTHHHHHHHHH
T ss_pred HHHHhhCchHHHHHHHh
Confidence 56999999999998754
No 38
>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=21.03 E-value=66 Score=25.31 Aligned_cols=44 Identities=9% Similarity=0.121 Sum_probs=29.6
Q ss_pred HhcCCCHHHHHHhHH-HHHHHhcCCCHHHHhcCCHHHHHH-hcccchhhc
Q 024277 200 ALSELTWPAILSKRH-IFREVFVGFDPIAVSKLNEKKLLA-AGSAASSLL 247 (270)
Q Consensus 200 fQAGLSW~tILkKRe-~FReAF~gFDp~kVA~~~E~~Ie~-Ll~d~~IIR 247 (270)
.+.|..|..+++++. .|++.. -.....++++++.. |+++|.+|+
T Consensus 43 ~~~~~~~~~lin~~~~~~k~l~----~~~~~~~s~~e~i~~l~~~p~Lik 88 (110)
T PF03960_consen 43 SKLGNGPDDLINTRSKTYKELG----KLKKDDLSDEELIELLLENPKLIK 88 (110)
T ss_dssp HHHTSSGGGGB-TTSHHHHHTT----HHHCTTSBHHHHHHHHHHSGGGB-
T ss_pred HHhcccHHHHhcCccchHhhhh----hhhhhhhhhHHHHHHHHhChhhee
Confidence 456788999999994 555554 45567888888765 556777665
No 39
>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=20.71 E-value=90 Score=24.89 Aligned_cols=54 Identities=17% Similarity=0.063 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhcCCCHHHHHHhHHHHHHHhcCCCHH-HHhcCCHHHH-HHhcccchhhc
Q 024277 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPI-AVSKLNEKKL-LAAGSAASSLL 247 (270)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~FReAF~gFDp~-kVA~~~E~~I-e~Ll~d~~IIR 247 (270)
-.+-|.--..+.|..|..++++|... |...... ++..++++++ +-+++++.+|+
T Consensus 37 ~~~el~~l~~~~~~~~~~lin~~~~~---~k~l~~~~~~~~ls~~e~~~~i~~~p~Lik 92 (117)
T TIGR01617 37 TREELLDILSLLEDGIDPLLNTRGQS---YRALNTSNTFLDLSDKEALELLAEDPALLR 92 (117)
T ss_pred hHHHHHHHHHHcCCCHHHheeCCCcc---hhhCCchhhcccCCHHHHHHHHHhCcceEe
Confidence 34444444456788999999998754 3344443 3677886665 45666776665
No 40
>PRK04038 rps19p 30S ribosomal protein S19P; Provisional
Probab=20.36 E-value=85 Score=27.27 Aligned_cols=24 Identities=8% Similarity=0.200 Sum_probs=21.7
Q ss_pred HhcCCCHHHHhcCCHHHHHHhccc
Q 024277 219 VFVGFDPIAVSKLNEKKLLAAGSA 242 (270)
Q Consensus 219 AF~gFDp~kVA~~~E~~Ie~Ll~d 242 (270)
.|-|+|++.+-+|+.+++..|+..
T Consensus 8 ~yrG~~l~~L~~m~~~~~~~l~~a 31 (134)
T PRK04038 8 TYRGYTLEELQEMSLEEFAELLPA 31 (134)
T ss_pred eecccCHHHHHcCCHHHHHHHcch
Confidence 478999999999999999998875
No 41
>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=20.02 E-value=98 Score=22.18 Aligned_cols=48 Identities=15% Similarity=0.208 Sum_probs=30.7
Q ss_pred HHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccchhhcchhHHHHHHH
Q 024277 209 ILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIE 257 (270)
Q Consensus 209 ILkKRe~FReAF~gFDp~kVA~~~E~~Ie~Ll~d~~IIRNr~KI~AVI~ 257 (270)
|+...+.|.+||...|++.++.+=.++..-. ...+-+..+..+.+.+.
T Consensus 1 I~a~~~~~~~A~~~~D~~~~~~~~~~d~~~~-~~~g~~~~~~~~l~~~~ 48 (107)
T PF14534_consen 1 IRALEEQYEDAFNAGDIDALASLYADDFVFV-GPGGTILGKEAILAAFK 48 (107)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHTTEEEEEEEE-ETTSEEEEHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCHHHHHhhhCCCEEEE-CCCCCEeCHHHHHHHHh
Confidence 6677889999999999999987744443222 22333445555544443
Done!