Query 027832
Match_columns 218
No_of_seqs 185 out of 880
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 15:53:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027832hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2875 8-oxoguanine DNA glyco 100.0 3.4E-53 7.3E-58 368.7 12.5 183 33-217 3-189 (323)
2 TIGR00588 ogg 8-oxoguanine DNA 100.0 4.3E-45 9.2E-50 327.7 17.1 181 36-217 3-191 (310)
3 PF07934 OGG_N: 8-oxoguanine D 100.0 9.3E-33 2E-37 215.0 9.7 111 40-151 1-117 (117)
4 PRK10308 3-methyl-adenine DNA 99.9 1.9E-24 4.1E-29 192.1 16.5 143 66-217 31-183 (283)
5 COG0122 AlkA 3-methyladenine D 99.9 2.5E-22 5.5E-27 178.6 8.1 108 99-217 62-172 (285)
6 KOG1918 3-methyladenine DNA gl 99.3 6E-12 1.3E-16 107.5 6.3 88 121-217 48-138 (254)
7 PF00730 HhH-GPD: HhH-GPD supe 99.1 3.9E-11 8.5E-16 91.2 2.9 53 152-217 1-59 (108)
8 TIGR01083 nth endonuclease III 99.0 4.1E-10 8.9E-15 94.7 5.8 76 128-217 5-87 (191)
9 PRK10702 endonuclease III; Pro 99.0 7.7E-10 1.7E-14 94.8 6.1 74 130-217 10-90 (211)
10 cd00056 ENDO3c endonuclease II 98.9 5E-10 1.1E-14 90.6 3.6 56 148-217 1-61 (158)
11 TIGR01084 mutY A/G-specific ad 98.6 2.9E-08 6.3E-13 88.3 4.7 60 144-217 23-86 (275)
12 PRK10880 adenine DNA glycosyla 98.2 9.6E-07 2.1E-11 81.1 4.6 60 144-217 27-90 (350)
13 PRK13913 3-methyladenine DNA g 98.1 5E-06 1.1E-10 71.8 5.1 67 144-217 27-98 (218)
14 PF06029 AlkA_N: AlkA N-termin 97.8 3.3E-05 7.1E-10 60.5 5.4 75 66-143 31-112 (116)
15 COG0177 Nth Predicted EndoIII- 97.7 8.5E-05 1.9E-09 63.8 6.2 76 128-217 8-90 (211)
16 TIGR03252 uncharacterized HhH- 97.4 0.00034 7.3E-09 58.7 5.4 50 144-206 15-65 (177)
17 PRK01229 N-glycosylase/DNA lya 95.7 0.019 4.2E-07 49.3 5.3 29 144-172 34-62 (208)
18 COG1194 MutY A/G-specific DNA 94.3 0.041 8.9E-07 50.6 3.4 58 145-216 32-93 (342)
19 smart00478 ENDO3c endonuclease 92.5 0.045 9.8E-07 43.5 0.6 18 156-173 1-18 (149)
20 COG2231 Uncharacterized protei 87.9 1.3 2.8E-05 38.2 5.5 46 148-206 31-76 (215)
21 KOG1921 Endonuclease III [Repl 74.8 5.5 0.00012 35.4 4.7 58 147-217 78-140 (286)
22 PF14520 HHH_5: Helix-hairpin- 58.9 15 0.00032 24.7 3.4 23 190-212 26-49 (60)
23 TIGR00624 tag DNA-3-methyladen 54.1 51 0.0011 27.7 6.5 71 123-206 5-77 (179)
24 PF04539 Sigma70_r3: Sigma-70 51.1 25 0.00055 24.4 3.7 33 162-206 3-39 (78)
25 PF09999 DUF2240: Uncharacteri 48.6 46 0.00099 27.1 5.2 36 144-179 83-120 (144)
26 PF11549 Sec31: Protein transp 48.2 2.9 6.2E-05 28.0 -1.5 28 19-46 2-34 (51)
27 PRK10353 3-methyl-adenine DNA 47.1 73 0.0016 27.0 6.4 71 123-206 6-78 (187)
28 PLN03132 NADH dehydrogenase (u 46.9 11 0.00023 36.3 1.5 18 15-32 13-30 (461)
29 PF06568 DUF1127: Domain of un 46.2 16 0.00035 22.9 1.8 19 192-210 16-34 (40)
30 PF11239 DUF3040: Protein of u 45.0 37 0.00081 24.4 3.8 24 116-139 11-34 (82)
31 PF12921 ATP13: Mitochondrial 41.3 48 0.001 26.0 4.2 69 98-179 17-86 (126)
32 PF09597 IGR: IGR protein moti 41.2 11 0.00024 25.9 0.5 29 189-217 18-48 (57)
33 PF03352 Adenine_glyco: Methyl 41.0 45 0.00097 28.0 4.2 71 124-207 2-74 (179)
34 PF03385 DUF288: Protein of un 39.3 15 0.00033 34.3 1.2 39 162-201 153-196 (390)
35 COG1059 Thermostable 8-oxoguan 37.3 40 0.00088 28.9 3.3 57 145-217 37-96 (210)
36 COG1379 PHP family phosphoeste 36.9 56 0.0012 30.4 4.4 63 143-212 301-364 (403)
37 PF12826 HHH_2: Helix-hairpin- 33.9 28 0.00062 23.8 1.6 24 189-212 22-46 (64)
38 PF11608 Limkain-b1: Limkain b 31.2 55 0.0012 24.6 2.8 39 160-198 14-54 (90)
39 PRK11508 sulfur transfer prote 27.4 57 0.0012 25.3 2.5 61 128-192 25-90 (109)
40 PF13592 HTH_33: Winged helix- 27.3 80 0.0017 21.2 3.0 20 192-215 23-43 (60)
41 KOG2841 Structure-specific end 26.5 26 0.00057 30.9 0.5 30 187-216 212-243 (254)
42 KOG1945 Protein phosphatase 1 26.4 36 0.00078 31.8 1.4 15 148-162 261-275 (377)
43 PF09268 Clathrin-link: Clathr 26.2 80 0.0017 18.0 2.3 23 149-171 2-24 (24)
44 KOG2675 Adenylate cyclase-asso 25.8 52 0.0011 31.6 2.3 50 134-198 415-465 (480)
45 PF07647 SAM_2: SAM domain (St 25.0 69 0.0015 21.3 2.3 20 191-210 31-50 (66)
46 COG3168 PilP Tfp pilus assembl 24.3 2.4E+02 0.0053 23.5 5.7 35 48-82 98-140 (170)
47 PRK12283 tryptophanyl-tRNA syn 23.0 3.1E+02 0.0067 26.0 6.9 83 115-211 308-398 (398)
48 PF00550 PP-binding: Phosphopa 22.1 80 0.0017 20.7 2.2 32 164-198 33-65 (67)
49 TIGR03342 dsrC_tusE_dsvC sulfu 22.0 66 0.0014 24.8 1.9 64 128-195 24-93 (108)
50 PRK13482 DNA integrity scannin 20.0 97 0.0021 28.9 2.9 28 189-216 306-335 (352)
No 1
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=100.00 E-value=3.4e-53 Score=368.72 Aligned_cols=183 Identities=40% Similarity=0.788 Sum_probs=167.4
Q ss_pred cCCCCceeccCCCCCcCcCccccCCCccceeEeCCCeeEEeeCCeEEEEEEcCCCcEEEEEeCCCC--hHHHHHHHHhhh
Q 027832 33 NKPSKWTPLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHTSPS--EPAAKSALLDFL 110 (218)
Q Consensus 33 ~~~~~w~~l~~~~~~~~L~~tL~sGQ~FrW~~~~~~~~~gvi~~~vv~lrq~~~~~l~~~~~~~~~--~~~~~~~l~~yF 110 (218)
.+...|.+|+++.++++|+.||.+||+|||++.+.+.|+||+|+.+|.++|+++..+.|.+.++.+ .++..+.|++||
T Consensus 3 ~t~~~w~~i~~~~sEl~L~~tL~sGQsFRWr~~~~~~ysG~lg~~v~~L~Q~ee~~~~y~~~~s~~~p~~del~~i~~yf 82 (323)
T KOG2875|consen 3 STPALWASIPCSRSELDLELTLPSGQSFRWREQSPAHYSGVLGDQVWTLTQTEEQCTVYRGDKSASRPTPDELEAISKYF 82 (323)
T ss_pred CccccceeccCCHHHcchhhhccCCceeeeecCCcccccceeccEEEEEEecCCceEEEEeecCCCCCChHHHHHHHHHH
Confidence 345579999999999999999999999999999889999999999999999876546677766522 234455899999
Q ss_pred ccCCChHHHHHHhhccChhHHHHHHhcCCcccCCCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeec
Q 027832 111 NMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHE 189 (218)
Q Consensus 111 ~Ld~dl~~~~~~~~~~Dp~l~~~~~~~~GlRilrqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~ 189 (218)
+||++|..+|.+|...|++|.++.. .|+|+|||||||||+||||||||||+||++|+++|| .||.+|+.++|.+||.
T Consensus 83 ~ldv~L~~l~~~W~~~D~~F~~la~--qgvRlLrQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~ 160 (323)
T KOG2875|consen 83 QLDVTLAQLYHHWGSVDDHFQELAQ--QGVRLLRQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHG 160 (323)
T ss_pred hheeeHHHHHHHhCcCChHHHHHHH--hhhHHHhcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCccccc
Confidence 9999999999999999999999998 799999999999999999999999999999999999 8999999999999999
Q ss_pred CCCHHHHh-cCCHHHHHHCCCCccccccc
Q 027832 190 FPSLERLS-LVSEVELRNAGFGYRCFAIK 217 (218)
Q Consensus 190 FPtpe~La-~~~~e~LR~~g~GyRA~yI~ 217 (218)
|||.++|+ ...|++||++|||||||||.
T Consensus 161 FPsl~~L~g~~~Ea~LR~~gfGYRAkYI~ 189 (323)
T KOG2875|consen 161 FPSLQALAGPEVEAELRKLGFGYRAKYIS 189 (323)
T ss_pred CccHHHhcCcHhHHHHHHcCcchhHHHHH
Confidence 99999999 46799999999999999996
No 2
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=100.00 E-value=4.3e-45 Score=327.75 Aligned_cols=181 Identities=36% Similarity=0.732 Sum_probs=160.6
Q ss_pred CCceeccCCCCCcCcCccccCCCcccee-EeCCCeeEE--eeCCe-EEEEEEcCCCcEEEEEeC-C-CChHHHHHHHHhh
Q 027832 36 SKWTPLNLTQSELSLPLTFPTGQTFRWK-KTGPLQYTG--PIGPH-LISLKHLQNGDVCYHIHT-S-PSEPAAKSALLDF 109 (218)
Q Consensus 36 ~~w~~l~~~~~~~~L~~tL~sGQ~FrW~-~~~~~~~~g--vi~~~-vv~lrq~~~~~l~~~~~~-~-~~~~~~~~~l~~y 109 (218)
..|.+|+++..+|||+.||+|||||||+ +.+++.|.+ ++++. ++.++|.++ .+.+.+.. . ...+.+.+.+++|
T Consensus 3 ~~w~~~~~~~~~~~l~~tl~~GQ~Frw~~~~~~~~y~~~~~~~~~~~~~~~q~~~-~~~~~~~~~~~~~~~~~~~~ir~~ 81 (310)
T TIGR00588 3 HRWASIPIPRSELRLDLVLRSGQSFRWRWEESPAHWSGLLVIADQPVWTLTQTEE-QLLCTVYRGDKPTQDELETKLEKY 81 (310)
T ss_pred CcccccCCchhcccHHHHcCCCceecCceeCCCCeEEEEEEECCeeEEEEEEcCC-ceEEEEecCCCccHHHHHHHHHHH
Confidence 5899999999999999999999999998 777789999 77877 889998754 34333332 2 1245678899999
Q ss_pred hccCCChHHHHHHhhccChhHHHHHHhcCCcccCCCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceee
Q 027832 110 LNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFH 188 (218)
Q Consensus 110 F~Ld~dl~~~~~~~~~~Dp~l~~~~~~~~GlRilrqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y 188 (218)
|+||.|++.++++|..+||.|++++++++|+|+++|||||+||+||||||+|+++|++++++|+ .||+++.+++|..+|
T Consensus 82 f~Ld~d~~~i~~~~~~~D~~l~~~~~~~~GlRi~~~d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~ 161 (310)
T TIGR00588 82 FQLDVSLAQLYTHWGSVDKHFQYVAQKFQGVRLLRQDPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYH 161 (310)
T ss_pred hcCCCCHHHHHHHHhhcCHHHHHHHHhCCCCCCCCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccc
Confidence 9999999999999977899999999999999999999999999999999999999999999999 799988777888899
Q ss_pred cCCCHHHHhcCC-HHHHHHCCCCccccccc
Q 027832 189 EFPSLERLSLVS-EVELRNAGFGYRCFAIK 217 (218)
Q Consensus 189 ~FPtpe~La~~~-~e~LR~~g~GyRA~yI~ 217 (218)
.||||++|++.. +++||.|||||||+||+
T Consensus 162 ~FPtp~~La~~~~e~~Lr~~G~g~Ra~~I~ 191 (310)
T TIGR00588 162 GFPSLHALTGPEAEAHLRKLGLGYRARYIR 191 (310)
T ss_pred cCCCHHHHhCCChHHHHHHcCCHHHHHHHH
Confidence 999999999875 67999999999999985
No 3
>PF07934 OGG_N: 8-oxoguanine DNA glycosylase, N-terminal domain; InterPro: IPR012904 The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (3.2.2.23 from EC) and DNA lyase activity (4.2.99.18 from EC) []. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket []. ; GO: 0003684 damaged DNA binding, 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006289 nucleotide-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 1N39_A 1LWV_A 1YQM_A 2NOL_A 1YQL_A 1LWY_A ....
Probab=99.98 E-value=9.3e-33 Score=214.99 Aligned_cols=111 Identities=32% Similarity=0.594 Sum_probs=86.9
Q ss_pred eccCCCCCcCcCccccCCCccceeEeCCCeeEEeeCCeEEEEEEcCCCcEEEEEeC------CCChHHHHHHHHhhhccC
Q 027832 40 PLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHT------SPSEPAAKSALLDFLNMG 113 (218)
Q Consensus 40 ~l~~~~~~~~L~~tL~sGQ~FrW~~~~~~~~~gvi~~~vv~lrq~~~~~l~~~~~~------~~~~~~~~~~l~~yF~Ld 113 (218)
+|+++..+|||+.||+|||+|||++.+++.|+||+++++|.|+|.+ +.+.|.+.. ..+.++..+.|++||+||
T Consensus 1 ~l~~~~~~~~L~~tL~sGQ~FrW~~~~~~~~~gv~~~~~~~l~q~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~YF~Ld 79 (117)
T PF07934_consen 1 KLPIPKEEFNLDKTLFSGQSFRWRKIDDGEWSGVIGDRVVQLRQDD-DNLLYRCLSSAEPSNSSSEEDIEEFLRDYFDLD 79 (117)
T ss_dssp EEE-STTT--HHHHCCTTS-SSEEEECTTEEEEEETTEEEEEEEET-TEEEEECE--TTS---S-HHHHHHCHHHHTTTT
T ss_pred CCcCCHHHcCHHHHhcccCcccCEEeCCCeEEEEcCCeEEEEEECC-CEEEEEEecCCCcccccchhhHHHHHHHHhcCC
Confidence 5788899999999999999999999987779999999999999974 566666543 123567889999999999
Q ss_pred CChHHHHHHhhccChhHHHHHHhcCCcccCCCChHHHH
Q 027832 114 ISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECL 151 (218)
Q Consensus 114 ~dl~~~~~~~~~~Dp~l~~~~~~~~GlRilrqdpfE~L 151 (218)
+||+++|++|+++|+.|+.+++.++|||||+|||||||
T Consensus 80 ~dl~~l~~~~~~~D~~l~~~~~~~~GlRiLrQdp~E~L 117 (117)
T PF07934_consen 80 VDLEKLYEDWSKKDPRLAKAIDKYRGLRILRQDPFETL 117 (117)
T ss_dssp S-HHHHHHHHCCHSHHHHHHHHCTTT-------HHHHH
T ss_pred ccHHHHHHHHhhhCHHHHHHHhcCCCcEEECCChhhhC
Confidence 99999999999889999999999999999999999997
No 4
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.92 E-value=1.9e-24 Score=192.07 Aligned_cols=143 Identities=15% Similarity=0.158 Sum_probs=117.2
Q ss_pred CCCeeEEee----CCeEEEEEEcCCCc-EEEEEeCCC--ChHHHHHHHHhhhccCCChHHHHHHhhccChhHHHHHHhcC
Q 027832 66 GPLQYTGPI----GPHLISLKHLQNGD-VCYHIHTSP--SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLA 138 (218)
Q Consensus 66 ~~~~~~gvi----~~~vv~lrq~~~~~-l~~~~~~~~--~~~~~~~~l~~yF~Ld~dl~~~~~~~~~~Dp~l~~~~~~~~ 138 (218)
+++.|..++ +.-++.|++.++.. +..++..+. ....+...+++|||||.|++.|++.+ +.+++..+
T Consensus 31 ~~~~y~R~~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L-------~~~~~~~~ 103 (283)
T PRK10308 31 AEGYYARSLAVGEHRGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGAL-------GKLGAARP 103 (283)
T ss_pred ECCEEEEEEEECCccEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHH-------HHHHHhCC
Confidence 456677655 35678888865432 555555432 23457899999999999999998655 56899999
Q ss_pred Cccc-CCCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCCHHHHHHCCCCc-cccc
Q 027832 139 GARV-LRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGY-RCFA 215 (218)
Q Consensus 139 GlRi-lrqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~g~Gy-RA~y 215 (218)
|+|+ .++||||+++++|||||+|+++|++++++|+ .||+++.+ +..++.|||||+|+++++++|++||+|+ ||+|
T Consensus 104 GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~--~~~~~~FPtpe~La~~~~~eL~~~Gl~~~Ra~~ 181 (283)
T PRK10308 104 GLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDD--FPEYVCFPTPERLAAADPQALKALGMPLKRAEA 181 (283)
T ss_pred CCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccC--CCCccCCCCHHHHHcCCHHHHHHCCCCHHHHHH
Confidence 9999 4799999999999999999999999999999 79998743 2347999999999999999999999996 7999
Q ss_pred cc
Q 027832 216 IK 217 (218)
Q Consensus 216 I~ 217 (218)
|+
T Consensus 182 L~ 183 (283)
T PRK10308 182 LI 183 (283)
T ss_pred HH
Confidence 85
No 5
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.87 E-value=2.5e-22 Score=178.64 Aligned_cols=108 Identities=25% Similarity=0.392 Sum_probs=96.3
Q ss_pred hHHHHHHHHhhhccCCChHHHHHHhhccChhHHHHHHhcCCccc-CCCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhC
Q 027832 99 EPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARV-LRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLG 176 (218)
Q Consensus 99 ~~~~~~~l~~yF~Ld~dl~~~~~~~~~~Dp~l~~~~~~~~GlRi-lrqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G 176 (218)
.+++...+.++|+||.||..+++++. .|+.... +|+|+ +++||||||+++|||||+|+++|.+|++||+ .||
T Consensus 62 ~~~~~~~~~~~~~lD~~l~~i~~~~~-~~~~~~~-----~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g 135 (285)
T COG0122 62 AEDIEAALRRLFDLDPDLAPIIDALG-PLPLLRA-----PGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYG 135 (285)
T ss_pred hHHHHHHHHHHHhcCCcHHHHHHhcC-ccccccc-----cCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhC
Confidence 46788999999999999999998876 5665544 67776 7999999999999999999999999999999 799
Q ss_pred CCcccccCceeecCCCHHHHhcCCHHHHHHCCC-Cccccccc
Q 027832 177 SHLGNVEGFEFHEFPSLERLSLVSEVELRNAGF-GYRCFAIK 217 (218)
Q Consensus 177 ~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~g~-GyRA~yI~ 217 (218)
+.+. .+|+|||||+|+++++++||.||+ ||||+||+
T Consensus 136 ~~~~-----~~~~fptpe~l~~~~~~~l~~~g~s~~Ka~yi~ 172 (285)
T COG0122 136 NALE-----IYHSFPTPEQLAAADEEALRRCGLSGRKAEYII 172 (285)
T ss_pred Cccc-----cccCCCCHHHHHhcCHHHHHHhCCcHHHHHHHH
Confidence 9873 689999999999999999999887 59999986
No 6
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.27 E-value=6e-12 Score=107.52 Aligned_cols=88 Identities=19% Similarity=0.239 Sum_probs=78.9
Q ss_pred HHhhccChhHHHHHHhcCCccc-CCCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhc
Q 027832 121 EGFSASDCRFAELAKYLAGARV-LRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSL 198 (218)
Q Consensus 121 ~~~~~~Dp~l~~~~~~~~GlRi-lrqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~ 198 (218)
.|+...||.|..++..+..++. -.|.|||.|+++|.|||.+-+++..+.+|++ .||.. +.||+||.+..
T Consensus 48 ~hl~~kd~~L~~lv~~~~p~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~---------~~~~~pe~i~~ 118 (254)
T KOG1918|consen 48 SHLDEKDPSLVKLVGNHEPLTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGA---------EKFPTPEFIDP 118 (254)
T ss_pred HhhhhcchHHHHHhcCCCCCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---------cCCCCchhcCc
Confidence 4666789999999999988888 6799999999999999999999999999999 58762 46999999999
Q ss_pred CCHHHHHHCCCCcc-ccccc
Q 027832 199 VSEVELRNAGFGYR-CFAIK 217 (218)
Q Consensus 199 ~~~e~LR~~g~GyR-A~yI~ 217 (218)
++.++||+|||+-| +.||.
T Consensus 119 ~~~~~lrkcG~S~rK~~yLh 138 (254)
T KOG1918|consen 119 LDCEELRKCGFSKRKASYLH 138 (254)
T ss_pred CCHHHHHHhCcchhhHHHHH
Confidence 99999999999988 78875
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=99.11 E-value=3.9e-11 Score=91.17 Aligned_cols=53 Identities=32% Similarity=0.409 Sum_probs=49.2
Q ss_pred HHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCCHHHHHHC----CCC-ccccccc
Q 027832 152 LQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA----GFG-YRCFAIK 217 (218)
Q Consensus 152 isfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~----g~G-yRA~yI~ 217 (218)
|++|++||++++++.+++++|+ .|| ||||++|+++++++|+++ ||+ +||+||+
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g-------------~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~ 59 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYG-------------FPTPEALAEASEEELRELIRPLGFSRRKAKYII 59 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHS-------------CSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHH
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhc-------------CCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHH
Confidence 6899999999999999999999 788 899999999999999998 999 9999985
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=99.02 E-value=4.1e-10 Score=94.67 Aligned_cols=76 Identities=18% Similarity=0.193 Sum_probs=62.8
Q ss_pred hhHHHHHHhcCCccc--CCCChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHH-
Q 027832 128 CRFAELAKYLAGARV--LRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL- 204 (218)
Q Consensus 128 p~l~~~~~~~~GlRi--lrqdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~L- 204 (218)
+.+..+.+.+++.+. ..+||||+||++|+|||.+.+.+.++.++|. ..||+|++|+++++++|
T Consensus 5 ~i~~~l~~~~~~~~~~~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~--------------~~~pt~~~l~~~~~~~L~ 70 (191)
T TIGR01083 5 EILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLF--------------EVYPTPQALAQAGLEELE 70 (191)
T ss_pred HHHHHHHHHCCCCCcccCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHH--------------HHCCCHHHHHcCCHHHHH
Confidence 345566677777664 4589999999999999999999999998874 24799999999999998
Q ss_pred ---HHCCCC-ccccccc
Q 027832 205 ---RNAGFG-YRCFAIK 217 (218)
Q Consensus 205 ---R~~g~G-yRA~yI~ 217 (218)
|.+||. .||+||.
T Consensus 71 ~~ir~~G~~~~Ka~~i~ 87 (191)
T TIGR01083 71 EYIKSIGLYRNKAKNII 87 (191)
T ss_pred HHHHhcCChHHHHHHHH
Confidence 778875 5799985
No 9
>PRK10702 endonuclease III; Provisional
Probab=98.98 E-value=7.7e-10 Score=94.81 Aligned_cols=74 Identities=12% Similarity=0.089 Sum_probs=58.9
Q ss_pred HHHHHHhcCCc--ccCCCChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHHHHC
Q 027832 130 FAELAKYLAGA--RVLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA 207 (218)
Q Consensus 130 l~~~~~~~~Gl--RilrqdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~ 207 (218)
+..+.+.++.. ....+||||+||++|+|||.+...+.+.+.+|. +.||+||+|+++++++|+++
T Consensus 10 ~~~l~~~~~~~~~~~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~--------------~~~pt~e~l~~a~~~~l~~~ 75 (211)
T PRK10702 10 LTRLRDNNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLY--------------PVANTPAAMLELGVEGVKTY 75 (211)
T ss_pred HHHHHHHCCCCCCCCCCCChHHHHHHHHHHhhcCHHHHHHHHHHHH--------------HHcCCHHHHHCCCHHHHHHH
Confidence 34444555532 235689999999999999999999999998872 45899999999999999885
Q ss_pred --CCCc---cccccc
Q 027832 208 --GFGY---RCFAIK 217 (218)
Q Consensus 208 --g~Gy---RA~yI~ 217 (218)
++|| ||+||.
T Consensus 76 i~~~G~y~~kA~~l~ 90 (211)
T PRK10702 76 IKTIGLYNSKAENVI 90 (211)
T ss_pred HHHcCCHHHHHHHHH
Confidence 6675 799875
No 10
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=98.95 E-value=5e-10 Score=90.55 Aligned_cols=56 Identities=25% Similarity=0.249 Sum_probs=52.4
Q ss_pred HHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCCHHHHHHCCCC----ccccccc
Q 027832 148 VECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFG----YRCFAIK 217 (218)
Q Consensus 148 fE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~g~G----yRA~yI~ 217 (218)
||+|+++||+||++++++.+++++|+ .|| ||||+|+.+++++|++|+.+ +||+||.
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g--------------pt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~ 61 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG--------------PTPEALAAADEEELRELIRSLGYRRKAKYLK 61 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC--------------CCHHHHHCCCHHHHHHHHHhcChHHHHHHHH
Confidence 79999999999999999999999998 677 89999999999999999987 7799885
No 11
>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=98.64 E-value=2.9e-08 Score=88.29 Aligned_cols=60 Identities=15% Similarity=0.298 Sum_probs=52.5
Q ss_pred CCChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHH----HHCCCCccccccc
Q 027832 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL----RNAGFGYRCFAIK 217 (218)
Q Consensus 144 rqdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~L----R~~g~GyRA~yI~ 217 (218)
.+||||.||+.|++||.+++++.....+|. ..|||+++|+++++++| +.+|+..||+||.
T Consensus 23 ~~dpy~vlvseIL~QQT~v~~v~~~~~rl~--------------~~fpt~~~La~a~~eeL~~~~~~lG~y~RAr~L~ 86 (275)
T TIGR01084 23 NKTPYRVWLSEVMLQQTQVATVIPYFERFL--------------ERFPTVQALANAPQDEVLKLWEGLGYYARARNLH 86 (275)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHH--------------HhCCCHHHHHCcCHHHHHHHHHHCCcHHHHHHHH
Confidence 469999999999999999999999999885 24799999999999999 6666655899875
No 12
>PRK10880 adenine DNA glycosylase; Provisional
Probab=98.25 E-value=9.6e-07 Score=81.06 Aligned_cols=60 Identities=18% Similarity=0.370 Sum_probs=53.2
Q ss_pred CCChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHHHH--CCCCc--cccccc
Q 027832 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN--AGFGY--RCFAIK 217 (218)
Q Consensus 144 rqdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~--~g~Gy--RA~yI~ 217 (218)
..|||+.+|+.|.+||.++.......++|.+ .|||+++||++++++|.+ .|+|| ||+||.
T Consensus 27 ~~dpy~ilVseILlQQT~v~~v~~~~~rl~~--------------~fPt~~~La~a~~eel~~~~~glGyy~RAr~L~ 90 (350)
T PRK10880 27 DKTPYKVWLSEVMLQQTQVATVIPYFERFMA--------------RFPTVTDLANAPLDEVLHLWTGLGYYARARNLH 90 (350)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHHH--------------HCcCHHHHHCcCHHHHHHHHHcCChHHHHHHHH
Confidence 4699999999999999999999999988852 479999999999999988 58887 899885
No 13
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=98.07 E-value=5e-06 Score=71.78 Aligned_cols=67 Identities=15% Similarity=0.138 Sum_probs=53.6
Q ss_pred CCChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHHHHC----CCCcc-ccccc
Q 027832 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA----GFGYR-CFAIK 217 (218)
Q Consensus 144 rqdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~----g~GyR-A~yI~ 217 (218)
+.+|||.||+.|++||.+-.+..+.+.+|..-|.-. -..||+|+.|+++++++|+++ ||..+ |+||.
T Consensus 27 ~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~-------~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk 98 (218)
T PRK13913 27 NALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILE-------NDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLI 98 (218)
T ss_pred CcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccc-------cccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHH
Confidence 569999999999999999999999999886321100 013699999999999999988 88754 88875
No 14
>PF06029 AlkA_N: AlkA N-terminal domain; InterPro: IPR010316 This domain is found at the N terminus of bacterial AlkA 3.2.2.21 from EC. AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove []. This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision []. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [].; GO: 0003905 alkylbase DNA N-glycosylase activity; PDB: 1MPG_B 3CWS_D 3CW7_C 3CWA_B 3D4V_A 3CWT_C 3CWU_B 3OGD_A 3CVS_C 1PVS_A ....
Probab=97.84 E-value=3.3e-05 Score=60.48 Aligned_cols=75 Identities=17% Similarity=0.232 Sum_probs=47.4
Q ss_pred CCCeeEEee--C--CeEEEEEEcCC-CcEEEEEeCCC--ChHHHHHHHHhhhccCCChHHHHHHhhccChhHHHHHHhcC
Q 027832 66 GPLQYTGPI--G--PHLISLKHLQN-GDVCYHIHTSP--SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLA 138 (218)
Q Consensus 66 ~~~~~~gvi--~--~~vv~lrq~~~-~~l~~~~~~~~--~~~~~~~~l~~yF~Ld~dl~~~~~~~~~~Dp~l~~~~~~~~ 138 (218)
+++.|...+ + .-+|.++..++ +.+..++..+. ....+...++++||||.|+..|.+++ ||.++..+...+
T Consensus 31 ~~~~Y~Rt~~l~~~~g~v~v~~~~~~~~l~v~~~~~~~~~l~~~~~rvRrlfDLdaDp~~I~~~L---dp~l~p~~~~~p 107 (116)
T PF06029_consen 31 DDGSYRRTFRLGGGPGWVSVRHDPEKNHLRVTLSLSDLRDLPAVIARVRRLFDLDADPQAIEAHL---DPLLAPLVAARP 107 (116)
T ss_dssp ESSEEEEEEEETTEEEEEEEEEETTTTEEEEEE-GGGGGGHHHHHHHHHHHTTTT--HHHHHHHH-------GGGGTS-T
T ss_pred eCCeEEEEEEeCCeEEEEEEEEcCCCCEEEEEEEcccHHHHHHHHHHHHHHhCCCCCHHHHHHHH---hhcccccccCCC
Confidence 455777655 2 34788887653 34677776432 34567889999999999999999999 899999999999
Q ss_pred CcccC
Q 027832 139 GARVL 143 (218)
Q Consensus 139 GlRil 143 (218)
|+|+.
T Consensus 108 GLRlP 112 (116)
T PF06029_consen 108 GLRLP 112 (116)
T ss_dssp T----
T ss_pred CCcCC
Confidence 99994
No 15
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=97.69 E-value=8.5e-05 Score=63.84 Aligned_cols=76 Identities=24% Similarity=0.306 Sum_probs=58.7
Q ss_pred hhHHHHHHhcCCccc-CC-CChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHH-
Q 027832 128 CRFAELAKYLAGARV-LR-QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL- 204 (218)
Q Consensus 128 p~l~~~~~~~~GlRi-lr-qdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~L- 204 (218)
..+..+.+.++.-+. +. .||||.||..|+|||..=.+.-+...+|- -.|||||+|+++++++|
T Consensus 8 ~i~~~l~~~~p~~~~~l~~~~pf~lLva~iLSaqttD~~vn~at~~Lf--------------~~~~t~e~l~~a~~~~l~ 73 (211)
T COG0177 8 EILDRLRELYPEPKTELDFKDPFELLVAVILSAQTTDEVVNKATPALF--------------KRYPTPEDLLNADEEELE 73 (211)
T ss_pred HHHHHHHHHCCCCCCccCcCCcHHHHHHHHHhccCchHHHHHHHHHHH--------------HHcCCHHHHHcCCHHHHH
Confidence 344555666776666 55 79999999999999998888887777773 23579999999998776
Q ss_pred ---HHCCCCcc-ccccc
Q 027832 205 ---RNAGFGYR-CFAIK 217 (218)
Q Consensus 205 ---R~~g~GyR-A~yI~ 217 (218)
|.+||--+ ||||+
T Consensus 74 ~~I~~iGlyr~KAk~I~ 90 (211)
T COG0177 74 ELIKSIGLYRNKAKNIK 90 (211)
T ss_pred HHHHhcCCcHHHHHHHH
Confidence 45788655 88885
No 16
>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=97.37 E-value=0.00034 Score=58.66 Aligned_cols=50 Identities=18% Similarity=0.178 Sum_probs=44.8
Q ss_pred CCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCCHHHHHH
Q 027832 144 RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN 206 (218)
Q Consensus 144 rqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~ 206 (218)
..+|||.||..|+|||.+-..+.+.+.+|. ++|. ++|+.|+++++++|.+
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~-------------~tp~~La~a~~eeL~~ 65 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGS-------------LDAEDIAKYDPQAFVA 65 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCC-------------CCHHHHHcCCHHHHHH
Confidence 468999999999999999999999999996 6764 5899999999888866
No 17
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=95.73 E-value=0.019 Score=49.28 Aligned_cols=29 Identities=14% Similarity=0.040 Sum_probs=26.9
Q ss_pred CCChHHHHHHHHHHhcccHHHHHHHHHHH
Q 027832 144 RQDPVECLLQFLCSSNNNIARITKMVDFL 172 (218)
Q Consensus 144 rqdpfE~LisfI~sQn~nI~~i~~~i~rL 172 (218)
..||||.|+..|+|||.+-....+..++|
T Consensus 34 ~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L 62 (208)
T PRK01229 34 EEDLFSELSFCILTANSSAEGGIKAQKEI 62 (208)
T ss_pred cCChHHHHHHHHhcCcCcHHHHHHHHHhc
Confidence 46999999999999999999999999888
No 18
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.31 E-value=0.041 Score=50.55 Aligned_cols=58 Identities=19% Similarity=0.398 Sum_probs=45.4
Q ss_pred CChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHHHH--CCCCcc--cccc
Q 027832 145 QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN--AGFGYR--CFAI 216 (218)
Q Consensus 145 qdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~--~g~GyR--A~yI 216 (218)
.+||..++|-|..||..+.+......+.. -.|||+++||+++++++.. -|+||- |+.+
T Consensus 32 ~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl--------------~rfPti~~LA~A~~~evl~~W~gLGYysRArnL 93 (342)
T COG1194 32 KDPYRVWVSEIMLQQTQVATVIPYYERFL--------------ERFPTIKALAAAPEDEVLKAWEGLGYYSRARNL 93 (342)
T ss_pred CCcceehhHHHHhhhccHhhhhhhHHHHH--------------HhCCCHHHHhcCCHHHHHHHHHhcChHHHHHHH
Confidence 47999999999999998887766665553 2589999999998776655 788854 5543
No 19
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=92.52 E-value=0.045 Score=43.52 Aligned_cols=18 Identities=17% Similarity=0.111 Sum_probs=16.8
Q ss_pred HHhcccHHHHHHHHHHHH
Q 027832 156 CSSNNNIARITKMVDFLA 173 (218)
Q Consensus 156 ~sQn~nI~~i~~~i~rL~ 173 (218)
+|||++++.+.+++++|.
T Consensus 1 l~qq~~~~~a~~~~~~l~ 18 (149)
T smart00478 1 LSQQTSDEAVNKATERLF 18 (149)
T ss_pred CCCcccHHHHHHHHHHHH
Confidence 589999999999999997
No 20
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=87.93 E-value=1.3 Score=38.23 Aligned_cols=46 Identities=20% Similarity=0.284 Sum_probs=40.2
Q ss_pred HHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHHHH
Q 027832 148 VECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN 206 (218)
Q Consensus 148 fE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~ 206 (218)
.|.++++|+.||.|.+.+.+.+++|...|.- .+++|..+++++|.+
T Consensus 31 ~EiiigAILtQNT~WknvekAlenLk~~~~~-------------~l~~I~~~~~~~L~e 76 (215)
T COG2231 31 DEIIIGAILTQNTSWKNVEKALENLKNEGIL-------------NLKKILKLDEEELAE 76 (215)
T ss_pred hhHHHHHHHhccccHHHHHHHHHHHHHcccC-------------CHHHHhcCCHHHHHH
Confidence 4999999999999999999999999865532 489999999888877
No 21
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=74.84 E-value=5.5 Score=35.43 Aligned_cols=58 Identities=22% Similarity=0.240 Sum_probs=44.6
Q ss_pred hHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHHHH----CCCCcc-ccccc
Q 027832 147 PVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN----AGFGYR-CFAIK 217 (218)
Q Consensus 147 pfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~----~g~GyR-A~yI~ 217 (218)
=|..|+..++|+|.-=..-...+.||..+|. -|+|.+.+.++..|.+ .||=-| |+||.
T Consensus 78 RfqvLv~lmLSSQTKDevt~~Am~rL~~~~g-------------LT~e~v~~~de~~l~~LI~~VgFy~rKA~ylk 140 (286)
T KOG1921|consen 78 RFQVLVGLMLSSQTKDEVTAAAMLRLKEYGG-------------LTLEAVLKIDEPTLNELIYPVGFYTRKAKYLK 140 (286)
T ss_pred hHHHHHHHHHhcchHHHHHHHHHHHHHHhcC-------------CCHHHHhccChHhHHhhhhhccchHHHHHHHH
Confidence 4789999999999877777777778877772 2899999999888777 345444 78874
No 22
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=58.89 E-value=15 Score=24.68 Aligned_cols=23 Identities=30% Similarity=0.463 Sum_probs=19.7
Q ss_pred CCCHHHHhcCCHHHHHH-CCCCcc
Q 027832 190 FPSLERLSLVSEVELRN-AGFGYR 212 (218)
Q Consensus 190 FPtpe~La~~~~e~LR~-~g~GyR 212 (218)
|.|+++|+.+++++|.+ -|+|-+
T Consensus 26 ~~t~~~l~~a~~~~L~~i~Gig~~ 49 (60)
T PF14520_consen 26 IKTLEDLANADPEELAEIPGIGEK 49 (60)
T ss_dssp CSSHHHHHTSHHHHHHTSTTSSHH
T ss_pred CCcHHHHHcCCHHHHhcCCCCCHH
Confidence 45899999999999988 589865
No 23
>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=54.06 E-value=51 Score=27.73 Aligned_cols=71 Identities=4% Similarity=0.048 Sum_probs=52.0
Q ss_pred hhccChhHHHHHHhcCCcccC-CCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCC
Q 027832 123 FSASDCRFAELAKYLAGARVL-RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVS 200 (218)
Q Consensus 123 ~~~~Dp~l~~~~~~~~GlRil-rqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~ 200 (218)
|...||.+..--..--|.-+. .+..||.|+--+.....|...|-+-.+.+. .|... .|+.+|..+
T Consensus 5 W~~~~~l~~~YHD~eWG~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~F-------------d~~~VA~~~ 71 (179)
T TIGR00624 5 WASVDPLYRAYHDNEWGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSGF-------------DIVKVARMT 71 (179)
T ss_pred CcCCChHHHHhhhccCCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCC-------------CHHHHhCCC
Confidence 444555555544555676663 357999999999999999988888888776 56542 589999988
Q ss_pred HHHHHH
Q 027832 201 EVELRN 206 (218)
Q Consensus 201 ~e~LR~ 206 (218)
++++..
T Consensus 72 e~~ie~ 77 (179)
T TIGR00624 72 DADVER 77 (179)
T ss_pred HHHHHH
Confidence 887755
No 24
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=51.11 E-value=25 Score=24.38 Aligned_cols=33 Identities=27% Similarity=0.428 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhc---CCHHHHHH
Q 027832 162 IARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSL---VSEVELRN 206 (218)
Q Consensus 162 I~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~---~~~e~LR~ 206 (218)
+.+|.+..+.|. .+|.. ||.++||. ++.++++.
T Consensus 3 l~~i~~a~~~L~~~lgr~------------Pt~eEiA~~lgis~~~v~~ 39 (78)
T PF04539_consen 3 LRKIERARRELEQELGRE------------PTDEEIAEELGISVEEVRE 39 (78)
T ss_dssp HHHHHHHHHHHHHHHSS--------------BHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHHHHhCCC------------CCHHHHHHHHcccHHHHHH
Confidence 567888888887 68863 89999985 57777765
No 25
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=48.64 E-value=46 Score=27.08 Aligned_cols=36 Identities=22% Similarity=0.466 Sum_probs=32.4
Q ss_pred CCChHHHHHHHHHH-hcccHHHHHHHHHHHH-hhCCCc
Q 027832 144 RQDPVECLLQFLCS-SNNNIARITKMVDFLA-SLGSHL 179 (218)
Q Consensus 144 rqdpfE~LisfI~s-Qn~nI~~i~~~i~rL~-~~G~~i 179 (218)
.+|+||-++.+|.+ .+.+-..+..+++.+. +||..+
T Consensus 83 e~~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l 120 (144)
T PF09999_consen 83 ERDPFERILDYIAAKTGIEKQEVVAEINELQEELGGLL 120 (144)
T ss_pred cccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccC
Confidence 46999999999999 8899999999999988 799766
No 26
>PF11549 Sec31: Protein transport protein SEC31; InterPro: IPR021614 Sec31 is involved in COPII coat formation as it forms through the sequential binding of three cytoplasmic proteins: Sar1, Sec23/24 and Sec13/31. Sec13/31 is recruited by the pre-budding complex and polymerisation of Sec13/31 occurs to form an octahedral cage that is the outer shell of the COPII coat []. Sec13/31 is a hetero-tetramer which is organised as a linear array of alpha-solenoid and beta-propeller domains to form a rod in which twenty-four copies assemble to form the COPII cub-octahedron []. ; PDB: 2QTV_D.
Probab=48.23 E-value=2.9 Score=27.97 Aligned_cols=28 Identities=36% Similarity=0.750 Sum_probs=5.1
Q ss_pred CCCCCCCCccc-----ccccCCCCceeccCCCC
Q 027832 19 QPPPTPPNPQT-----LTTNKPSKWTPLNLTQS 46 (218)
Q Consensus 19 ~~~~~~~~~~~-----~~~~~~~~w~~l~~~~~ 46 (218)
.|||+++||.. +...-..+|++|++..+
T Consensus 2 ~~~p~~~~~~SGQ~PhlNkkaNdGWNDLpl~vk 34 (51)
T PF11549_consen 2 PPPPPPPNVYSGQTPHLNKKANDGWNDLPLKVK 34 (51)
T ss_dssp -----------SSS-TT-HHHHS-TT---S---
T ss_pred CCCCcccccccCcCCcccccccCcccccchhhh
Confidence 34555555532 23334568888887643
No 27
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=47.12 E-value=73 Score=27.00 Aligned_cols=71 Identities=7% Similarity=0.007 Sum_probs=52.7
Q ss_pred hhccChhHHHHHHhcCCcccC-CCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCC
Q 027832 123 FSASDCRFAELAKYLAGARVL-RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVS 200 (218)
Q Consensus 123 ~~~~Dp~l~~~~~~~~GlRil-rqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~ 200 (218)
|+..||.+..--..--|.-+- .+..||.|+=-......|...|-+-.+.+. .|... .|+.+|..+
T Consensus 6 W~~~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~F-------------d~~~VA~~~ 72 (187)
T PRK10353 6 WVSQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQF-------------DPVKVAAMQ 72 (187)
T ss_pred CCCCChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCC-------------CHHHHhCCC
Confidence 444566655555555687663 357999999999999999999988888887 56542 588888888
Q ss_pred HHHHHH
Q 027832 201 EVELRN 206 (218)
Q Consensus 201 ~e~LR~ 206 (218)
++++..
T Consensus 73 e~die~ 78 (187)
T PRK10353 73 EEDVER 78 (187)
T ss_pred HHHHHH
Confidence 877755
No 28
>PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional
Probab=46.93 E-value=11 Score=36.34 Aligned_cols=18 Identities=50% Similarity=0.995 Sum_probs=12.4
Q ss_pred CCCCCCCCCCCCcccccc
Q 027832 15 RLTPQPPPTPPNPQTLTT 32 (218)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~ 32 (218)
..||||||+||.|.+-+.
T Consensus 13 ~~~~~~~~~~~~~~~~~~ 30 (461)
T PLN03132 13 AATPQPPPPPPPPEKTHF 30 (461)
T ss_pred cCCCCCcccCCCCcccCC
Confidence 457888887777765443
No 29
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=46.23 E-value=16 Score=22.90 Aligned_cols=19 Identities=21% Similarity=0.371 Sum_probs=16.9
Q ss_pred CHHHHhcCCHHHHHHCCCC
Q 027832 192 SLERLSLVSEVELRNAGFG 210 (218)
Q Consensus 192 tpe~La~~~~e~LR~~g~G 210 (218)
+-.+|+++++.+|+.+|+.
T Consensus 16 tr~~L~~Lsd~~L~DIGl~ 34 (40)
T PF06568_consen 16 TRRELAELSDRQLADIGLT 34 (40)
T ss_pred HHHHHccCCHHHHHHcCCC
Confidence 5678999999999999986
No 30
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=44.98 E-value=37 Score=24.44 Aligned_cols=24 Identities=29% Similarity=0.223 Sum_probs=18.9
Q ss_pred hHHHHHHhhccChhHHHHHHhcCC
Q 027832 116 LGELWEGFSASDCRFAELAKYLAG 139 (218)
Q Consensus 116 l~~~~~~~~~~Dp~l~~~~~~~~G 139 (218)
|+++.+++..+||.|+...+..+.
T Consensus 11 L~eiEr~L~~~DP~fa~~l~~~~~ 34 (82)
T PF11239_consen 11 LEEIERQLRADDPRFAARLRSGRP 34 (82)
T ss_pred HHHHHHHHHhcCcHHHHHhccCCC
Confidence 467888998899999998877433
No 31
>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].
Probab=41.28 E-value=48 Score=25.95 Aligned_cols=69 Identities=13% Similarity=0.129 Sum_probs=44.8
Q ss_pred ChHHHHHHHHhhhccCCChHHHHHHhhccChhHHHHHHhcCCcccCCCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhC
Q 027832 98 SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLG 176 (218)
Q Consensus 98 ~~~~~~~~l~~yF~Ld~dl~~~~~~~~~~Dp~l~~~~~~~~GlRilrqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G 176 (218)
+.+.++..|.++.+.|.+-......+...+|. + .......+++.+. +.|++|..+-++++.+. .|+
T Consensus 17 ~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl-------~-----Pt~~lL~AIv~sf-~~n~~i~~al~~vd~fs~~Y~ 83 (126)
T PF12921_consen 17 QLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPL-------Y-----PTSRLLIAIVHSF-GYNGDIFSALKLVDFFSRKYP 83 (126)
T ss_pred CHHHHHHHHHHhcCCCCCCccccCccCCCCCC-------C-----CCHHHHHHHHHHH-HhcccHHHHHHHHHHHHHHcC
Confidence 34567788888888877643222111111111 1 2234567788777 88999999999999998 799
Q ss_pred CCc
Q 027832 177 SHL 179 (218)
Q Consensus 177 ~~i 179 (218)
-++
T Consensus 84 I~i 86 (126)
T PF12921_consen 84 IPI 86 (126)
T ss_pred CCC
Confidence 444
No 32
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=41.19 E-value=11 Score=25.86 Aligned_cols=29 Identities=31% Similarity=0.322 Sum_probs=25.0
Q ss_pred cCCC-HHHHhcCCHHHHHHCCCCccc-cccc
Q 027832 189 EFPS-LERLSLVSEVELRNAGFGYRC-FAIK 217 (218)
Q Consensus 189 ~FPt-pe~La~~~~e~LR~~g~GyRA-~yI~ 217 (218)
.|++ .++|-..+-.+|++.|+.-|. +||.
T Consensus 18 kf~~~w~~lf~~~s~~LK~~GIp~r~RryiL 48 (57)
T PF09597_consen 18 KFESDWEKLFTTSSKQLKELGIPVRQRRYIL 48 (57)
T ss_pred HHHHHHHHHHhcCHHHHHHCCCCHHHHHHHH
Confidence 4788 899999999999999998884 8874
No 33
>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=41.00 E-value=45 Score=28.04 Aligned_cols=71 Identities=14% Similarity=0.093 Sum_probs=48.7
Q ss_pred hccChhHHHHHHhcCCcccCC-CChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCCH
Q 027832 124 SASDCRFAELAKYLAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSE 201 (218)
Q Consensus 124 ~~~Dp~l~~~~~~~~GlRilr-qdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~~ 201 (218)
+..||.+..--...-|.-+.. +..||.|+--+.....|...|-+-...+. .|-.. .|+.+|..++
T Consensus 2 ~~~~~~~~~YHD~eWG~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~F-------------d~~~vA~~~e 68 (179)
T PF03352_consen 2 ANSDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAGF-------------DPEKVAKMDE 68 (179)
T ss_dssp TTSSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGGG-------------HHHHHHT--H
T ss_pred CCCChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHCC-------------CHHHHHcCCH
Confidence 334566655555666765533 46999999999999999999988888887 55432 5899999998
Q ss_pred HHHHHC
Q 027832 202 VELRNA 207 (218)
Q Consensus 202 e~LR~~ 207 (218)
+++.++
T Consensus 69 ~~ie~l 74 (179)
T PF03352_consen 69 EDIERL 74 (179)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 887664
No 34
>PF03385 DUF288: Protein of unknown function, DUF288; InterPro: IPR005049 This is a protein family of unknown function.
Probab=39.25 E-value=15 Score=34.30 Aligned_cols=39 Identities=21% Similarity=0.166 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhhCCCcccccCc-----eeecCCCHHHHhcCCH
Q 027832 162 IARITKMVDFLASLGSHLGNVEGF-----EFHEFPSLERLSLVSE 201 (218)
Q Consensus 162 I~~i~~~i~rL~~~G~~i~~~~g~-----~~y~FPtpe~La~~~~ 201 (218)
-+.+++..++|-.||+-+ ++..+ .-..||+|+||+...+
T Consensus 153 ~~~~~ra~qKlnyFGDl~-~WC~etg~s~~~~~fpsp~QL~~~h~ 196 (390)
T PF03385_consen 153 SQNIKRAEQKLNYFGDLV-DWCNETGYSNLSKYFPSPEQLAEQHD 196 (390)
T ss_pred cHHHHHHHHHHHhhchHH-HHHhccCCccccccCCCHHHHHHHhh
Confidence 466677777776778654 22111 1246999999997654
No 35
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.31 E-value=40 Score=28.90 Aligned_cols=57 Identities=21% Similarity=0.212 Sum_probs=38.9
Q ss_pred CChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhcCCHHHHHHCCC---Cccccccc
Q 027832 145 QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGF---GYRCFAIK 217 (218)
Q Consensus 145 qdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~g~---GyRA~yI~ 217 (218)
.+.|.-|.-.|...|.|-..+-++.+.| |+.+ +|. +.|+|.+ .|+.+|. +-||+||+
T Consensus 37 e~lf~ELsFCILTANsSA~~~~~~q~~l---G~gf-------ly~--~~eEL~e----~Lk~~g~Rf~n~raeyIV 96 (210)
T COG1059 37 EDLFKELSFCILTANSSATMGLRAQNEL---GDGF-------LYL--SEEELRE----KLKEVGYRFYNVRAEYIV 96 (210)
T ss_pred HHHHHHHHHHhccccchHHHHHHHHHHh---cccc-------ccC--CHHHHHH----HHHHhcchhcccchHHHH
Confidence 3577777778888888877777777665 5432 232 6777744 5888874 45689985
No 36
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=36.95 E-value=56 Score=30.43 Aligned_cols=63 Identities=14% Similarity=0.225 Sum_probs=45.3
Q ss_pred CCCChHHHHHHHHHHhcccHHHHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhcCCHHHHHHCCCCcc
Q 027832 143 LRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYR 212 (218)
Q Consensus 143 lrqdpfE~LisfI~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~~~~e~LR~~g~GyR 212 (218)
+++=|.+-+++--++-.+..+..++.+++|. +||..+.. -.--++|+||.+.+ ...++=..||
T Consensus 301 lhliPLaeIi~~~~g~gi~tK~V~~~we~lv~~FGtEi~v------Li~a~~e~La~V~~-~vA~aI~~~R 364 (403)
T COG1379 301 LHLIPLAEIISMALGKGITTKAVKRTWERLVRAFGTEIDV------LIDAPIEELARVDP-KVAEAIVAFR 364 (403)
T ss_pred eecccHHHHHHHHhccceechhHHHHHHHHHHHhcchhhh------HhcCCHHHHhhhhH-HHHHHHHHHh
Confidence 5667888777777788888899999999999 79998732 11236889988876 3333333444
No 37
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=33.94 E-value=28 Score=23.83 Aligned_cols=24 Identities=42% Similarity=0.462 Sum_probs=16.2
Q ss_pred cCCCHHHHhcCCHHHHHHC-CCCcc
Q 027832 189 EFPSLERLSLVSEVELRNA-GFGYR 212 (218)
Q Consensus 189 ~FPtpe~La~~~~e~LR~~-g~GyR 212 (218)
.|.+.+.|.+++.++|..+ |+|-.
T Consensus 22 ~f~sl~~l~~a~~e~L~~i~gIG~~ 46 (64)
T PF12826_consen 22 HFGSLEALMNASVEELSAIPGIGPK 46 (64)
T ss_dssp CCSCHHHHCC--HHHHCTSTT--HH
T ss_pred HcCCHHHHHHcCHHHHhccCCcCHH
Confidence 4678999999999999885 77754
No 38
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=31.18 E-value=55 Score=24.58 Aligned_cols=39 Identities=21% Similarity=0.270 Sum_probs=25.1
Q ss_pred ccHHHHHHHHHHHH-hhCCCcccc-cCceeecCCCHHHHhc
Q 027832 160 NNIARITKMVDFLA-SLGSHLGNV-EGFEFHEFPSLERLSL 198 (218)
Q Consensus 160 ~nI~~i~~~i~rL~-~~G~~i~~~-~g~~~y~FPtpe~La~ 198 (218)
...+.|+.-+.+|+ .+|.++..+ .+..+..|+++|.-..
T Consensus 14 ~d~~~I~~RL~qLsdNCGGkVl~v~~~tAilrF~~~~~A~R 54 (90)
T PF11608_consen 14 KDPSSIKNRLRQLSDNCGGKVLSVSGGTAILRFPNQEFAER 54 (90)
T ss_dssp S-HHHHHHHHHHHHHTTT--EEE--TT-EEEEESSHHHHHH
T ss_pred CCHHHHHHHHHHHhhccCCEEEEEeCCEEEEEeCCHHHHHH
Confidence 44677888888888 699887655 4455678999887443
No 39
>PRK11508 sulfur transfer protein TusE; Provisional
Probab=27.37 E-value=57 Score=25.28 Aligned_cols=61 Identities=23% Similarity=0.274 Sum_probs=41.0
Q ss_pred hhHHHHHHhcCCcccCCCChHHHHHHHH---HHhcccHHHHHHHHHHHH-hhCCCcccccCceee-cCCC
Q 027832 128 CRFAELAKYLAGARVLRQDPVECLLQFL---CSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFH-EFPS 192 (218)
Q Consensus 128 p~l~~~~~~~~GlRilrqdpfE~LisfI---~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y-~FPt 192 (218)
+.++..+++-.|+. |..+-||. |.|+ -.++.+.+.+|.++.-+. .+|...+. ...+| .||.
T Consensus 25 e~vA~~lA~~egie-LT~~HW~V-I~~lR~~y~e~~~~P~~R~l~K~~~~~~g~~k~~--~kyLy~LFP~ 90 (109)
T PRK11508 25 EPLAVVIAENEGIS-LSPEHWEV-VRFVRDFYLEFNTSPAIRMLVKAMANKFGEEKGN--SRYLYRLFPK 90 (109)
T ss_pred HHHHHHHHHHhCCC-CCHHHHHH-HHHHHHHHHHHCCCCcHHHHHHHHHHHhCccccc--HHHHHHHCCC
Confidence 66777777777863 77777773 3444 467778889999998887 68865421 12233 7996
No 40
>PF13592 HTH_33: Winged helix-turn helix
Probab=27.27 E-value=80 Score=21.18 Aligned_cols=20 Identities=25% Similarity=0.286 Sum_probs=13.6
Q ss_pred CHHHHhcCCHHHHHHCCCCcc-ccc
Q 027832 192 SLERLSLVSEVELRNAGFGYR-CFA 215 (218)
Q Consensus 192 tpe~La~~~~e~LR~~g~GyR-A~y 215 (218)
++..+.. -|+.+||+|+ .++
T Consensus 23 s~~~v~~----lL~r~G~s~~kp~~ 43 (60)
T PF13592_consen 23 SPSGVYR----LLKRLGFSYQKPRP 43 (60)
T ss_pred cHHHHHH----HHHHcCCccccCCC
Confidence 5666654 4888999987 344
No 41
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=26.46 E-value=26 Score=30.92 Aligned_cols=30 Identities=33% Similarity=0.486 Sum_probs=24.7
Q ss_pred eecCCCHHHHhcCCHHHHHH-CCCCcc-cccc
Q 027832 187 FHEFPSLERLSLVSEVELRN-AGFGYR-CFAI 216 (218)
Q Consensus 187 ~y~FPtpe~La~~~~e~LR~-~g~GyR-A~yI 216 (218)
+..|+|.++|.++++++|.. -|+|=+ |+-|
T Consensus 212 L~~FgsLq~~~~AS~~ele~~~G~G~~kak~l 243 (254)
T KOG2841|consen 212 LQKFGSLQQISNASEGELEQCPGLGPAKAKRL 243 (254)
T ss_pred HHhcccHHHHHhcCHhHHHhCcCcCHHHHHHH
Confidence 46799999999999999988 579966 5543
No 42
>KOG1945 consensus Protein phosphatase 1 binding protein spinophilin/neurabin II [Signal transduction mechanisms]
Probab=26.35 E-value=36 Score=31.75 Aligned_cols=15 Identities=13% Similarity=0.104 Sum_probs=10.7
Q ss_pred HHHHHHHHHHhcccH
Q 027832 148 VECLLQFLCSSNNNI 162 (218)
Q Consensus 148 fE~LisfI~sQn~nI 162 (218)
.|.+..+...|+-+-
T Consensus 261 lE~l~~~~k~q~~~~ 275 (377)
T KOG1945|consen 261 LELLVTWKKQQVYHW 275 (377)
T ss_pred hhhhhhhHHHHHHHH
Confidence 677888887766554
No 43
>PF09268 Clathrin-link: Clathrin, heavy-chain linker; InterPro: IPR015348 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the core motif for the alpha-helical zigzag linker region connecting the conserved N-terminal beta-propeller region to the C-terminal alpha-alpha-superhelical region in clathrin heavy chains []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 1C9I_A 1BPO_B 1C9L_A 1UTC_B 3GD1_I 3GC3_B 2XZG_A 2XZH_A.
Probab=26.25 E-value=80 Score=17.99 Aligned_cols=23 Identities=9% Similarity=0.179 Sum_probs=16.5
Q ss_pred HHHHHHHHHhcccHHHHHHHHHH
Q 027832 149 ECLLQFLCSSNNNIARITKMVDF 171 (218)
Q Consensus 149 E~LisfI~sQn~nI~~i~~~i~r 171 (218)
+.+|.||+.+=+|..-+-+|..|
T Consensus 2 ~~IVpyi~~~L~N~~LAl~lA~R 24 (24)
T PF09268_consen 2 ENIVPYILNTLQNPDLALRLASR 24 (24)
T ss_dssp TTHHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhHHHhccCCHHHHHHHhcC
Confidence 46899999999998888777543
No 44
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=25.76 E-value=52 Score=31.59 Aligned_cols=50 Identities=26% Similarity=0.361 Sum_probs=34.9
Q ss_pred HHhcCCccc-CCCChHHHHHHHHHHhcccHHHHHHHHHHHHhhCCCcccccCceeecCCCHHHHhc
Q 027832 134 AKYLAGARV-LRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSL 198 (218)
Q Consensus 134 ~~~~~GlRi-lrqdpfE~LisfI~sQn~nI~~i~~~i~rL~~~G~~i~~~~g~~~y~FPtpe~La~ 198 (218)
+.+.-|..| |.-|-.+|=|-.=+|+-+||..= ..++.+|--||=|||+..
T Consensus 415 I~ktdGc~iYLSk~sL~~eIvtsKSsemNi~vp---------------~~~dgDy~EfpvPEQfkt 465 (480)
T KOG2675|consen 415 IDKTDGCHIYLSKDSLDCEIVTSKSSEMNINVP---------------TNEDGDYVEFPVPEQFKT 465 (480)
T ss_pred EecCCCeeEEeccccccceEEeecccceeEecc---------------cCCCCCcccccChHHHhh
Confidence 344568888 88888888887777777765310 113456778999999865
No 45
>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=25.02 E-value=69 Score=21.32 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=17.1
Q ss_pred CCHHHHhcCCHHHHHHCCCC
Q 027832 191 PSLERLSLVSEVELRNAGFG 210 (218)
Q Consensus 191 Ptpe~La~~~~e~LR~~g~G 210 (218)
-..+.|+.+++++|+++|+.
T Consensus 31 ~g~~~L~~l~~~~L~~lGI~ 50 (66)
T PF07647_consen 31 DGLEDLLQLTEEDLKELGIT 50 (66)
T ss_dssp SHHHHHTTSCHHHHHHTTTT
T ss_pred cHHHHHhhCCHHHHHHcCCC
Confidence 34589999999999999984
No 46
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=24.26 E-value=2.4e+02 Score=23.45 Aligned_cols=35 Identities=20% Similarity=0.191 Sum_probs=24.3
Q ss_pred cCcCccccCCCcc-ceeEe-------CCCeeEEeeCCeEEEEE
Q 027832 48 LSLPLTFPTGQTF-RWKKT-------GPLQYTGPIGPHLISLK 82 (218)
Q Consensus 48 ~~L~~tL~sGQ~F-rW~~~-------~~~~~~gvi~~~vv~lr 82 (218)
|.|--||.+||.- -.-+. .-|.|.|...++|+.|.
T Consensus 98 ~rlvGtm~~g~~~~A~i~~~~~v~~V~vG~YlGqN~GrV~rI~ 140 (170)
T COG3168 98 FRLVGTLKSGQGVSALIEAPGGVYRVRVGQYLGQNYGRVVRIT 140 (170)
T ss_pred eeeEEEecCCCceEEEEEcCCceEEEeeccEeeccCceEEEec
Confidence 5566688898843 33333 34678888889999887
No 47
>PRK12283 tryptophanyl-tRNA synthetase; Reviewed
Probab=23.00 E-value=3.1e+02 Score=26.00 Aligned_cols=83 Identities=13% Similarity=0.201 Sum_probs=51.8
Q ss_pred ChHHHHHHhhccChhHHHHHHhcCCccc----CCCChHHHHHHHHHHhcccHHHHH---HHHHHHHhhCCCcccccCcee
Q 027832 115 SLGELWEGFSASDCRFAELAKYLAGARV----LRQDPVECLLQFLCSSNNNIARIT---KMVDFLASLGSHLGNVEGFEF 187 (218)
Q Consensus 115 dl~~~~~~~~~~Dp~l~~~~~~~~GlRi----lrqdpfE~LisfI~sQn~nI~~i~---~~i~rL~~~G~~i~~~~g~~~ 187 (218)
++-.+++.+. +|..+.++.+.+.+-++ +.+...|.++.++---+-...... ..+..+.+-|..
T Consensus 308 nl~~i~~~~~-~~~~~~~i~~~~~~g~~~~g~~K~~lae~v~e~L~~irer~~~~~~~~~~~~~il~~G~~--------- 377 (398)
T PRK12283 308 PVWQLHQVYS-DEETKEWVQKGCRSAGIGCLECKQPVIDAILREQQPMRERAQKYEDDPSLVRAIVADGCE--------- 377 (398)
T ss_pred HHHHHHHHhC-CChHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHH---------
Confidence 4455666663 45567788777754443 467888999988876665554442 223333344543
Q ss_pred ecCCCHHHHhcCCHHHHHH-CCCCc
Q 027832 188 HEFPSLERLSLVSEVELRN-AGFGY 211 (218)
Q Consensus 188 y~FPtpe~La~~~~e~LR~-~g~Gy 211 (218)
.+.++|..+-.+.|+ +||+|
T Consensus 378 ----kA~~~a~~t~~~v~~~~g~~~ 398 (398)
T PRK12283 378 ----KARKVARETMRDVREAMGLSY 398 (398)
T ss_pred ----HHHHHHHHHHHHHHHHhCCCC
Confidence 366777777777776 88887
No 48
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=22.10 E-value=80 Score=20.75 Aligned_cols=32 Identities=19% Similarity=0.358 Sum_probs=21.9
Q ss_pred HHHHHHHHHH-hhCCCcccccCceeecCCCHHHHhc
Q 027832 164 RITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSL 198 (218)
Q Consensus 164 ~i~~~i~rL~-~~G~~i~~~~g~~~y~FPtpe~La~ 198 (218)
.+..++..+. +||-.+ ....++.+||..+|++
T Consensus 33 ~~~~l~~~l~~~~g~~i---~~~~~~~~~ti~~l~~ 65 (67)
T PF00550_consen 33 DAIELVSELEEEFGIKI---PPSDLFEHPTIRDLAE 65 (67)
T ss_dssp HHHHHHHHHHHHHTSST---THHHHCTSSSHHHHHH
T ss_pred HHHHHHHHHHHHHcCCC---CHHHHHcCCCHHHHHh
Confidence 3445666666 688765 3346778899998875
No 49
>TIGR03342 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases.
Probab=22.00 E-value=66 Score=24.84 Aligned_cols=64 Identities=23% Similarity=0.283 Sum_probs=42.2
Q ss_pred hhHHHHHHhcCCcccCCCChHHHHHHHH---HHhcccHHHHHHHHHHHH-hhCCCcccccCceee-cCCC-HHH
Q 027832 128 CRFAELAKYLAGARVLRQDPVECLLQFL---CSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFH-EFPS-LER 195 (218)
Q Consensus 128 p~l~~~~~~~~GlRilrqdpfE~LisfI---~sQn~nI~~i~~~i~rL~-~~G~~i~~~~g~~~y-~FPt-pe~ 195 (218)
+.++.++++-.|+. |..+-||. |.|+ -.++...+.+|.++..+. .+|...+. ...+| .||. |..
T Consensus 24 e~vA~~lA~~egie-LT~~Hw~v-I~~lR~~y~e~~~~P~~R~l~K~~~~~~g~~kg~--~kyLy~LFP~gPak 93 (108)
T TIGR03342 24 EDVAEALAEEEGIE-LTEAHWEV-INFLRDFYAEYNISPAVRMLVKAMGKKLGEEKGN--SRYLYRLFPKGPAK 93 (108)
T ss_pred HHHHHHHHHHcCCC-CCHHHHHH-HHHHHHHHHHHCCCCcHHHHHHHHHHHhCccccc--HHHHHHHcCCCHHH
Confidence 66777777778873 77777773 3444 456778888899988887 68865321 12133 7986 544
No 50
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=20.05 E-value=97 Score=28.87 Aligned_cols=28 Identities=39% Similarity=0.477 Sum_probs=22.2
Q ss_pred cCCCHHHHhcCCHHHHHHC-CCC-cccccc
Q 027832 189 EFPSLERLSLVSEVELRNA-GFG-YRCFAI 216 (218)
Q Consensus 189 ~FPtpe~La~~~~e~LR~~-g~G-yRA~yI 216 (218)
.|-+.+.|.+++.++|.++ |+| .||+.|
T Consensus 306 ~FGSL~~Il~As~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 306 HFGSLQGLLAASIEDLDEVEGIGEVRARAI 335 (352)
T ss_pred HcCCHHHHHcCCHHHHhhCCCcCHHHHHHH
Confidence 4568999999999999984 788 566654
Done!