Query psy4725
Match_columns 457
No_of_seqs 237 out of 1999
Neff 4.5
Searched_HMMs 46136
Date Sat Aug 17 00:16:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2875|consensus 100.0 2.2E-78 4.7E-83 591.6 22.7 308 7-413 4-313 (323)
2 TIGR00588 ogg 8-oxoguanine DNA 100.0 1.2E-67 2.5E-72 528.7 30.4 299 9-404 3-308 (310)
3 COG0122 AlkA 3-methyladenine D 100.0 9.1E-40 2E-44 324.7 20.6 214 78-404 61-277 (285)
4 PRK10308 3-methyl-adenine DNA 100.0 1.1E-38 2.4E-43 316.5 27.1 236 46-401 32-276 (283)
5 PF07934 OGG_N: 8-oxoguanine D 100.0 6.5E-29 1.4E-33 215.6 10.1 113 13-131 1-117 (117)
6 cd00056 ENDO3c endonuclease II 99.9 5.7E-26 1.2E-30 204.4 13.0 152 128-399 1-157 (158)
7 TIGR01083 nth endonuclease III 99.9 7.3E-24 1.6E-28 198.8 16.3 159 109-393 6-171 (191)
8 PRK10702 endonuclease III; Pro 99.9 3.2E-23 7E-28 198.5 17.1 141 122-387 24-169 (211)
9 KOG1918|consensus 99.9 8.8E-22 1.9E-26 188.8 15.1 188 101-399 48-239 (254)
10 COG0177 Nth Predicted EndoIII- 99.9 3.1E-21 6.7E-26 185.1 17.4 170 110-403 10-187 (211)
11 smart00478 ENDO3c endonuclease 99.9 1.7E-21 3.6E-26 174.2 13.7 141 136-400 1-148 (149)
12 PRK13913 3-methyladenine DNA g 99.8 1.5E-20 3.3E-25 181.2 14.9 148 123-385 26-178 (218)
13 TIGR01084 mutY A/G-specific ad 99.8 3.5E-20 7.6E-25 184.0 17.4 158 124-401 23-186 (275)
14 PRK10880 adenine DNA glycosyla 99.8 9.3E-19 2E-23 179.1 17.4 156 124-399 27-188 (350)
15 PRK01229 N-glycosylase/DNA lya 99.7 1.7E-17 3.6E-22 159.3 14.0 161 123-400 33-202 (208)
16 PRK13910 DNA glycosylase MutY; 99.6 3.6E-15 7.7E-20 149.4 13.4 90 191-361 21-114 (289)
17 PF00730 HhH-GPD: HhH-GPD supe 99.5 3.1E-13 6.7E-18 114.6 11.6 61 132-227 1-66 (108)
18 TIGR03252 uncharacterized HhH- 99.5 4.5E-13 9.7E-18 126.0 12.4 101 124-259 15-126 (177)
19 COG1194 MutY A/G-specific DNA 99.3 1.3E-11 2.9E-16 125.9 12.9 123 125-363 32-157 (342)
20 COG2231 Uncharacterized protei 99.3 7.7E-11 1.7E-15 113.0 14.3 141 126-385 29-173 (215)
21 KOG1921|consensus 99.2 8.8E-11 1.9E-15 115.2 13.5 153 127-396 78-240 (286)
22 KOG2457|consensus 98.2 4.4E-06 9.5E-11 87.0 8.7 117 127-360 125-247 (555)
23 PF06029 AlkA_N: AlkA N-termin 97.8 3.3E-05 7.1E-10 68.4 5.9 76 45-123 31-112 (116)
24 COG1059 Thermostable 8-oxoguan 97.7 0.00066 1.4E-08 65.3 12.6 159 125-400 37-204 (210)
25 PF00633 HHH: Helix-hairpin-he 95.9 0.0054 1.2E-07 42.4 2.0 14 246-259 9-22 (30)
26 PF07934 OGG_N: 8-oxoguanine D 86.5 0.16 3.5E-06 44.2 -0.7 62 262-323 32-97 (117)
27 PRK13901 ruvA Holliday junctio 86.5 1.8 3.9E-05 42.1 6.4 59 187-264 57-123 (196)
28 smart00483 POLXc DNA polymeras 86.5 0.57 1.2E-05 48.4 3.1 54 206-264 49-105 (334)
29 PRK14600 ruvA Holliday junctio 84.8 0.55 1.2E-05 45.0 2.0 63 243-341 68-130 (186)
30 PRK14601 ruvA Holliday junctio 82.2 1.1 2.3E-05 43.0 2.8 25 242-266 67-91 (183)
31 smart00278 HhH1 Helix-hairpin- 81.9 0.66 1.4E-05 30.6 0.9 11 249-259 2-12 (26)
32 PRK14606 ruvA Holliday junctio 81.3 1.2 2.6E-05 42.8 2.7 25 242-266 67-91 (188)
33 PRK14606 ruvA Holliday junctio 80.5 2.4 5.3E-05 40.7 4.5 59 187-264 58-124 (188)
34 PRK14601 ruvA Holliday junctio 80.4 2.5 5.3E-05 40.6 4.5 59 187-264 58-124 (183)
35 PRK14605 ruvA Holliday junctio 80.3 1.1 2.5E-05 43.0 2.2 25 242-266 67-91 (194)
36 PRK14604 ruvA Holliday junctio 77.7 1.8 3.9E-05 41.8 2.7 25 242-266 67-91 (195)
37 TIGR00084 ruvA Holliday juncti 77.2 1.8 4E-05 41.5 2.6 25 242-266 66-90 (191)
38 PRK14605 ruvA Holliday junctio 76.9 3.4 7.3E-05 39.8 4.3 59 187-264 58-124 (194)
39 PF09674 DUF2400: Protein of u 76.2 3.2 7E-05 41.3 4.1 40 344-386 176-215 (232)
40 PRK14602 ruvA Holliday junctio 74.7 4.1 8.8E-05 39.6 4.3 59 187-264 59-125 (203)
41 PRK14604 ruvA Holliday junctio 73.3 4.3 9.4E-05 39.2 4.1 59 187-264 58-124 (195)
42 PRK14603 ruvA Holliday junctio 73.1 2.8 6.1E-05 40.5 2.7 25 242-266 66-90 (197)
43 PRK14603 ruvA Holliday junctio 72.6 4.7 0.0001 39.0 4.1 59 187-264 57-123 (197)
44 PRK14600 ruvA Holliday junctio 72.4 4.1 8.9E-05 39.1 3.6 58 187-264 58-123 (186)
45 COG0632 RuvA Holliday junction 72.4 5.4 0.00012 39.0 4.5 57 187-261 58-121 (201)
46 PRK14602 ruvA Holliday junctio 71.2 3 6.5E-05 40.5 2.5 25 242-266 68-92 (203)
47 TIGR00084 ruvA Holliday juncti 70.2 6.5 0.00014 37.8 4.5 65 187-264 57-123 (191)
48 TIGR02757 conserved hypothetic 68.0 6.2 0.00013 39.3 3.9 39 344-385 173-211 (229)
49 cd00141 NT_POLXc Nucleotidyltr 66.0 2.5 5.5E-05 43.2 0.8 48 211-264 52-101 (307)
50 PF12826 HHH_2: Helix-hairpin- 65.6 9.5 0.0002 30.2 3.8 34 222-261 15-48 (64)
51 COG1948 MUS81 ERCC4-type nucle 62.5 42 0.00091 34.1 8.6 106 128-259 75-193 (254)
52 PF14520 HHH_5: Helix-hairpin- 59.6 19 0.00042 27.8 4.5 15 245-259 2-16 (60)
53 PRK08609 hypothetical protein; 55.6 21 0.00045 39.7 5.7 47 207-259 50-99 (570)
54 PF14716 HHH_8: Helix-hairpin- 53.6 29 0.00064 27.6 4.8 39 211-259 20-58 (68)
55 PF03118 RNA_pol_A_CTD: Bacter 52.8 9.2 0.0002 30.8 1.7 42 207-259 14-55 (66)
56 PRK00116 ruvA Holliday junctio 49.2 23 0.00049 33.9 4.1 23 243-265 68-90 (192)
57 COG0353 RecR Recombinational D 48.1 17 0.00036 35.7 3.0 19 243-261 7-25 (198)
58 PRK00076 recR recombination pr 47.2 15 0.00031 35.9 2.5 17 243-259 6-22 (196)
59 COG2003 RadC DNA repair protei 45.1 16 0.00036 36.4 2.5 56 195-259 21-77 (224)
60 PRK13844 recombination protein 43.9 16 0.00035 35.8 2.2 20 242-261 9-28 (200)
61 TIGR00615 recR recombination p 43.5 21 0.00045 34.9 2.9 19 243-261 6-24 (195)
62 PF01367 5_3_exonuc: 5'-3' exo 40.3 2.8 6.1E-05 36.6 -3.2 18 249-266 19-36 (101)
63 PRK07758 hypothetical protein; 39.5 29 0.00064 30.4 2.9 25 231-259 54-78 (95)
64 PRK13901 ruvA Holliday junctio 37.3 10 0.00022 36.9 -0.3 25 242-266 66-90 (196)
65 PTZ00217 flap endonuclease-1; 36.1 8.2 0.00018 41.1 -1.2 57 249-328 236-292 (393)
66 PRK00116 ruvA Holliday junctio 33.9 24 0.00053 33.7 1.7 19 247-265 107-125 (192)
67 PF11372 DUF3173: Domain of un 33.8 1.2E+02 0.0026 24.5 5.3 49 205-253 7-57 (59)
68 PF11731 Cdd1: Pathogenicity l 33.6 31 0.00067 30.0 2.1 17 243-259 7-23 (93)
69 TIGR00608 radc DNA repair prot 32.7 24 0.00052 34.7 1.5 44 210-259 24-71 (218)
70 TIGR01259 comE comEA protein. 32.4 23 0.00049 31.6 1.1 15 247-261 67-81 (120)
71 PF10391 DNA_pol_lambd_f: Fing 32.1 7.3 0.00016 30.2 -1.8 19 248-266 2-20 (52)
72 PRK00024 hypothetical protein; 31.9 27 0.00059 34.4 1.7 49 205-259 28-77 (224)
73 COG1555 ComEA DNA uptake prote 31.8 18 0.00038 33.6 0.4 17 248-264 97-113 (149)
74 PF14520 HHH_5: Helix-hairpin- 31.7 60 0.0013 25.0 3.3 32 192-224 26-59 (60)
75 PRK07956 ligA NAD-dependent DN 31.1 74 0.0016 36.3 5.2 32 193-225 468-501 (665)
76 TIGR00575 dnlj DNA ligase, NAD 29.7 1.4E+02 0.0031 34.0 7.0 14 324-337 536-549 (652)
77 smart00483 POLXc DNA polymeras 26.6 78 0.0017 32.9 4.0 40 214-264 25-64 (334)
78 PF12836 HHH_3: Helix-hairpin- 25.6 1.1E+02 0.0024 24.1 3.9 41 204-259 13-55 (65)
79 cd00080 HhH2_motif Helix-hairp 25.4 19 0.0004 29.5 -0.6 19 248-266 22-40 (75)
80 PRK14976 5'-3' exonuclease; Pr 24.5 12 0.00027 37.9 -2.2 19 248-266 191-209 (281)
81 cd00141 NT_POLXc Nucleotidyltr 23.8 94 0.002 31.9 4.0 42 212-264 20-61 (307)
82 PF09862 DUF2089: Protein of u 23.8 3.1E+02 0.0066 24.8 6.7 46 191-250 62-112 (113)
83 PRK07945 hypothetical protein; 23.6 67 0.0014 33.3 2.9 43 213-264 21-65 (335)
84 KOG2841|consensus 22.8 81 0.0018 32.0 3.2 38 187-225 210-249 (254)
85 PF09999 DUF2240: Uncharacteri 21.7 1.6E+02 0.0035 27.6 4.7 37 124-160 83-120 (144)
86 PRK13482 DNA integrity scannin 21.1 2.1E+02 0.0047 30.5 6.0 39 189-228 304-344 (352)
87 PF09597 IGR: IGR protein moti 20.7 1.2E+02 0.0027 24.1 3.2 37 191-228 18-56 (57)
88 PF11798 IMS_HHH: IMS family H 20.5 38 0.00082 23.5 0.3 10 250-259 13-22 (32)
89 PRK09482 flap endonuclease-lik 20.4 31 0.00067 34.9 -0.3 19 248-266 182-200 (256)
90 COG4324 Predicted aminopeptida 20.1 1.3E+02 0.0029 31.3 4.1 98 280-393 207-312 (376)
91 PRK14973 DNA topoisomerase I; 20.1 2E+02 0.0042 34.5 6.0 65 191-259 822-888 (936)
No 1
>KOG2875|consensus
Probab=100.00 E-value=2.2e-78 Score=591.64 Aligned_cols=308 Identities=43% Similarity=0.768 Sum_probs=279.0
Q ss_pred ccccccccccCCcccccccccccccccceeecCCCCcccCCeEEEEECCeEEEEEEcCCe-EEEEEEeCCCCCHHHHHHH
Q psy4725 7 VHHLSGKILCPAIELSLTLTLLGGQSFRWKQLTSDEKKLGNRFQGVFKECVWTLWADPSY-LHYQVFSQHKLNANSVETM 85 (457)
Q Consensus 7 ~~~~~~~l~~~~~~l~L~~tL~~GQ~FrW~~~~~~~~~~~~~~~gv~~~~v~~l~q~~~~-L~y~~~~~~~~~~~~~~~~ 85 (457)
.+..|..|+|+..|++|+.||.+||+|||++.+ ...|.||+|++||.++|++.. +.|++....+.+..+..+.
T Consensus 4 t~~~w~~i~~~~sEl~L~~tL~sGQsFRWr~~~------~~~ysG~lg~~v~~L~Q~ee~~~~y~~~~s~~~p~~del~~ 77 (323)
T KOG2875|consen 4 TPALWASIPCSRSELDLELTLPSGQSFRWREQS------PAHYSGVLGDQVWTLTQTEEQCTVYRGDKSASRPTPDELEA 77 (323)
T ss_pred ccccceeccCCHHHcchhhhccCCceeeeecCC------cccccceeccEEEEEEecCCceEEEEeecCCCCCChHHHHH
Confidence 456799999999999999999999999999765 689999999999999999976 6677755533344455568
Q ss_pred HHHhhcCCCCHHHHHHHHhccChhHHHhhhhhCCccccCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCC
Q psy4725 86 LKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRMLNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDS 165 (457)
Q Consensus 86 lr~YFdLD~DL~~l~~~~~~~Dp~L~~li~~~~GLRILrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g 165 (457)
|+.||+||++|..+|.+|...|+.|..+.. .|+|+|||||||||||||||+||||+||++|+++||..||..|..++|
T Consensus 78 i~~yf~ldv~L~~l~~~W~~~D~~F~~la~--qgvRlLrQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg 155 (323)
T KOG2875|consen 78 ISKYFQLDVTLAQLYHHWGSVDDHFQELAQ--QGVRLLRQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDG 155 (323)
T ss_pred HHHHHhheeeHHHHHHHhCcCChHHHHHHH--hhhHHHhcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecC
Confidence 999999999999999999999999999988 699999999999999999999999999999999999999999998888
Q ss_pred CCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChHHHHHhcCCchhHHHHHHHHHHHHHcCCC-CcchhhcCCCHH
Q psy4725 166 DGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQGGGE-SWLERLGGKSYE 244 (457)
Q Consensus 166 ~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~Ee~LR~~g~gYRAkyI~~~A~~~~e~~G~-~~l~~l~~~~~~ 244 (457)
..||.|||.++|+....|+.||++|||||||||.++|++|.+.+|. .||++|++++||
T Consensus 156 ---------------------~~~h~FPsl~~L~g~~~Ea~LR~~gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~ye 214 (323)
T KOG2875|consen 156 ---------------------VDYHGFPSLQALAGPEVEAELRKLGFGYRAKYISATARALQEKQGGLAWLQSLRKSSYE 214 (323)
T ss_pred ---------------------cccccCccHHHhcCcHhHHHHHHcCcchhHHHHHHHHHHHHHhcccchHHHHHhcccHH
Confidence 7899999999999767899999999999999999999999996555 899999999999
Q ss_pred HHHHHhhcCCCccccCCCcccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhc
Q psy4725 245 EAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQ 324 (457)
Q Consensus 245 eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 324 (457)
||+++|+.+||||+|
T Consensus 215 ear~~L~~lpGVG~K----------------------------------------------------------------- 229 (323)
T KOG2875|consen 215 EAREALCSLPGVGPK----------------------------------------------------------------- 229 (323)
T ss_pred HHHHHHhcCCCCcch-----------------------------------------------------------------
Confidence 999999999999999
Q ss_pred cCChHHHHHHHHHhcCCCCccccchhHHHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhhcCcHHHHHHHHHhcccccc
Q psy4725 325 TCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFGKYAGWAHSILFCADLKKF 404 (457)
Q Consensus 325 ~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~~ag~A~~~lf~~~l~~~ 404 (457)
||||||||||+++++||||+||+|||.+.+++.....|.++|+.|.++..+|.++||+||||||.+||.+...-+
T Consensus 230 -----VADCI~Lm~l~~~~~VPVDvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~~~~G~YAGwAQ~~lfsa~~~m~ 304 (323)
T KOG2875|consen 230 -----VADCICLMSLDKLSAVPVDVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFRSLWGEYAGWAQAVLFSAQKSMV 304 (323)
T ss_pred -----HhhhhhhhhcCCCCcccchhhHHHHhhcccCCCccccccCCcchhHHHHHHHHHHhcccccchhheeeccchhhh
Confidence 999999999999999999999999999777777777778999999999999999999999999999997665555
Q ss_pred ccCCCcccc
Q psy4725 405 QAKPGEEKV 413 (457)
Q Consensus 405 ~~~~~~~~~ 413 (457)
+..+...++
T Consensus 305 ~~~s~~~~k 313 (323)
T KOG2875|consen 305 QSTSAPATK 313 (323)
T ss_pred cccccccch
Confidence 554444433
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=1.2e-67 Score=528.71 Aligned_cols=299 Identities=44% Similarity=0.825 Sum_probs=267.7
Q ss_pred ccccccccCCccccccccccccccccee-ecCCCCcccCCeEEE--EECCe-EEEEEEcCCeEEEEEEeCCCCCHHHHHH
Q psy4725 9 HLSGKILCPAIELSLTLTLLGGQSFRWK-QLTSDEKKLGNRFQG--VFKEC-VWTLWADPSYLHYQVFSQHKLNANSVET 84 (457)
Q Consensus 9 ~~~~~l~~~~~~l~L~~tL~~GQ~FrW~-~~~~~~~~~~~~~~g--v~~~~-v~~l~q~~~~L~y~~~~~~~~~~~~~~~ 84 (457)
+.|.+|.++..+|||+.||.|||||||+ +.+ ++.|.+ ++++. ++.++|.++.+.+..+.......+.+.+
T Consensus 3 ~~w~~~~~~~~~~~l~~tl~~GQ~Frw~~~~~------~~~y~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~ 76 (310)
T TIGR00588 3 HRWASIPIPRSELRLDLVLRSGQSFRWRWEES------PAHWSGLLVIADQPVWTLTQTEEQLLCTVYRGDKPTQDELET 76 (310)
T ss_pred CcccccCCchhcccHHHHcCCCceecCceeCC------CCeEEEEEEECCeeEEEEEEcCCceEEEEecCCCccHHHHHH
Confidence 6899999999999999999999999998 555 578999 77877 9999998776655544443335677889
Q ss_pred HHHHhhcCCCCHHHHHHHHhccChhHHHhhhhhCCccccCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccC
Q psy4725 85 MLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRMLNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLD 164 (457)
Q Consensus 85 ~lr~YFdLD~DL~~l~~~~~~~Dp~L~~li~~~~GLRILrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~ 164 (457)
++++||+||.|++.+++.|...||.|+++++.++|+|+++|||||+||+||||||+|+++|++++++|+++||+++...+
T Consensus 77 ~ir~~f~Ld~d~~~i~~~~~~~D~~l~~~~~~~~GlRi~~~d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~ 156 (310)
T TIGR00588 77 KLEKYFQLDVSLAQLYTHWGSVDKHFQYVAQKFQGVRLLRQDPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLD 156 (310)
T ss_pred HHHHHhcCCCCHHHHHHHHhhcCHHHHHHHHhCCCCCCCCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCC
Confidence 99999999999999999998899999999999999999999999999999999999999999999999999998875444
Q ss_pred CCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChHHHHHhcCCchhHHHHHHHHHHHHHcC-CCCcchhhcCCCH
Q psy4725 165 SDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVEAKLRQLGFGYRAKFIQKSAEYIIQGG-GESWLERLGGKSY 243 (457)
Q Consensus 165 g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~Ee~LR~~g~gYRAkyI~~~A~~~~e~~-G~~~l~~l~~~~~ 243 (457)
| ..+|.||||++|+..+.++.||.|||||||+||+++|+++.++. |..+++.|+++++
T Consensus 157 g---------------------~~~~~FPtp~~La~~~~e~~Lr~~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~ 215 (310)
T TIGR00588 157 G---------------------VTYHGFPSLHALTGPEAEAHLRKLGLGYRARYIRETARALLEEQGGRAWLQQIRGASY 215 (310)
T ss_pred C---------------------cccccCCCHHHHhCCChHHHHHHcCCHHHHHHHHHHHHHHHhccCCchhHHhhccCCh
Confidence 4 56899999999998766778999999999999999999999853 4458899999999
Q ss_pred HHHHHHhhcCCCccccCCCcccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhh
Q psy4725 244 EEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFR 323 (457)
Q Consensus 244 ~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 323 (457)
+++++.|++|||||||
T Consensus 216 ~~~~~~L~~l~GIG~~---------------------------------------------------------------- 231 (310)
T TIGR00588 216 EDAREALCELPGVGPK---------------------------------------------------------------- 231 (310)
T ss_pred HHHHHHHHhCCCccHH----------------------------------------------------------------
Confidence 9999999999999999
Q ss_pred ccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhcccC--CCCCCCCCHHHHHHHHHHHHhhhcCcHHHHHHHHHhccc
Q psy4725 324 QTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQ--KSTSKTLTPAVYNQIRAFFADKFGKYAGWAHSILFCADL 401 (457)
Q Consensus 324 ~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~~~--~~~~~~lt~~~y~~i~~~~~~~fg~~ag~A~~~lf~~~l 401 (457)
|||||+||+++++++||||+||+|++.++|... ..+.++++++.|++|++++++.||+|+||||+|||++++
T Consensus 232 ------tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~~~~g~~ag~aq~~lf~~~~ 305 (310)
T TIGR00588 232 ------VADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFRSLWGPYAGWAQAVLFSADL 305 (310)
T ss_pred ------HHHHHHHHhCCCCCceeecHHHHHHHHHHhcccccccccccCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHh
Confidence 999999999999999999999999999999643 223456789999999999999999999999999999998
Q ss_pred ccc
Q psy4725 402 KKF 404 (457)
Q Consensus 402 ~~~ 404 (457)
..+
T Consensus 306 ~~~ 308 (310)
T TIGR00588 306 RQG 308 (310)
T ss_pred hcc
Confidence 765
No 3
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.1e-40 Score=324.75 Aligned_cols=214 Identities=26% Similarity=0.371 Sum_probs=185.9
Q ss_pred CHHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHhhhhhCCccc-cCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHh
Q psy4725 78 NANSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRM-LNQDLTENIFSFLCSSNNNIARISGMIDKMCKEY 156 (457)
Q Consensus 78 ~~~~~~~~lr~YFdLD~DL~~l~~~~~~~Dp~L~~li~~~~GLRI-LrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~y 156 (457)
..+++...+.++|+||.+|..+++.+ ..|+.... +|+|+ +++||||+||++|||||+|+++|.+|++||++.|
T Consensus 61 ~~~~~~~~~~~~~~lD~~l~~i~~~~-~~~~~~~~-----~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~ 134 (285)
T COG0122 61 VAEDIEAALRRLFDLDPDLAPIIDAL-GPLPLLRA-----PGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLY 134 (285)
T ss_pred hhHHHHHHHHHHHhcCCcHHHHHHhc-Cccccccc-----cCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHh
Confidence 45678899999999999999999887 46766655 66665 7999999999999999999999999999999999
Q ss_pred CCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChHHHHHhcCC-chhHHHHHHHHHHHHHcCCCCcc
Q psy4725 157 GTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVEAKLRQLGF-GYRAKFIQKSAEYIIQGGGESWL 235 (457)
Q Consensus 157 Ge~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~Ee~LR~~g~-gYRAkyI~~~A~~~~e~~G~~~l 235 (457)
|..+ ..+|.||||++|+..+ ++.|+.||+ ||||+||+++|+++.+ |+..+
T Consensus 135 g~~~--------------------------~~~~~fptpe~l~~~~-~~~l~~~g~s~~Ka~yi~~~A~~~~~--g~~~~ 185 (285)
T COG0122 135 GNAL--------------------------EIYHSFPTPEQLAAAD-EEALRRCGLSGRKAEYIISLARAAAE--GELDL 185 (285)
T ss_pred CCcc--------------------------ccccCCCCHHHHHhcC-HHHHHHhCCcHHHHHHHHHHHHHHHc--CCccH
Confidence 9876 2589999999999986 678998887 7999999999999999 88889
Q ss_pred hhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhh
Q psy4725 236 ERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEW 315 (457)
Q Consensus 236 ~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 315 (457)
..+..++++++++.|++|||||||
T Consensus 186 ~~l~~~~~e~a~e~L~~i~GIG~W-------------------------------------------------------- 209 (285)
T COG0122 186 SELKPLSDEEAIEELTALKGIGPW-------------------------------------------------------- 209 (285)
T ss_pred HHhccCCHHHHHHHHHcCCCcCHH--------------------------------------------------------
Confidence 999999999999999999999999
Q ss_pred hchhhhhhccCChHHHHHHHHHhcCCCCcccc-chhHHHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhhcCcHHHHHH
Q psy4725 316 SNRDAFFRQTCGDFVADCICLMSLSHLQAVPV-DTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFGKYAGWAHS 394 (457)
Q Consensus 316 ~~~~~~~~~~~~~~vAdci~l~~l~~~~~~Pv-D~~v~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~~ag~A~~ 394 (457)
||||++||+|+++++||+ |+++++.+.++| ... +..++ .....+.+.||||+|||+.
T Consensus 210 --------------TAe~~llf~lgr~dvfP~~D~~lr~~~~~~~-~~~---~~~~~----~~~~~~~e~w~p~rs~A~~ 267 (285)
T COG0122 210 --------------TAEMFLLFGLGRPDVFPADDLGLRRAIKKLY-RLP---TRPTE----KEVRELAERWGPYRSYAAL 267 (285)
T ss_pred --------------HHHHHHHHcCCCCCCCChHHHHHHHHHHHHh-cCC---CCchH----HHHHHHHhcccCHHHHHHH
Confidence 999999999999999997 789988888877 221 12333 2245678999999999999
Q ss_pred HHHhcccccc
Q psy4725 395 ILFCADLKKF 404 (457)
Q Consensus 395 ~lf~~~l~~~ 404 (457)
|||++.....
T Consensus 268 yLw~~~~~~~ 277 (285)
T COG0122 268 YLWRYARATT 277 (285)
T ss_pred HHHHhhhccc
Confidence 9999865443
No 4
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=100.00 E-value=1.1e-38 Score=316.49 Aligned_cols=236 Identities=20% Similarity=0.246 Sum_probs=195.1
Q ss_pred CCeEEEEE----CCeEEEEEEcCCe--EEEEEEeCCCCCHHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHhhhhhCC
Q psy4725 46 GNRFQGVF----KECVWTLWADPSY--LHYQVFSQHKLNANSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVG 119 (457)
Q Consensus 46 ~~~~~gv~----~~~v~~l~q~~~~--L~y~~~~~~~~~~~~~~~~lr~YFdLD~DL~~l~~~~~~~Dp~L~~li~~~~G 119 (457)
++.|...+ +..+++|.++++. +..++..+.......+..++++|||||.|+..|++.+ ++++..++|
T Consensus 32 ~~~y~R~~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L-------~~~~~~~~G 104 (283)
T PRK10308 32 EGYYARSLAVGEHRGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGAL-------GKLGAARPG 104 (283)
T ss_pred CCEEEEEEEECCccEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHH-------HHHHHhCCC
Confidence 56787776 4778899988764 4444433322234568999999999999999998755 578999999
Q ss_pred cccc-CCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHH
Q psy4725 120 IRML-NQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDAL 198 (457)
Q Consensus 120 LRIL-rqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~L 198 (457)
+|++ .+||||+++++|||||+|++.++++..+|+++||+++.. + ..++.||||++|
T Consensus 105 lR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~--~---------------------~~~~~FPtpe~L 161 (283)
T PRK10308 105 LRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDD--F---------------------PEYVCFPTPERL 161 (283)
T ss_pred CcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccC--C---------------------CCccCCCCHHHH
Confidence 9995 799999999999999999999999999999999998731 1 247899999999
Q ss_pred cCCChHHHHHhcCCch-hHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCc
Q psy4725 199 ARPAVEAKLRQLGFGY-RAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPS 277 (457)
Q Consensus 199 A~~~~Ee~LR~~g~gY-RAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~ 277 (457)
++++ +++|+.||+++ ||+||+++|+++.+ |+..++.. .++++++++|++|||||||
T Consensus 162 a~~~-~~eL~~~Gl~~~Ra~~L~~lA~~i~~--g~l~l~~~--~~~~~~~~~L~~LpGIGpw------------------ 218 (283)
T PRK10308 162 AAAD-PQALKALGMPLKRAEALIHLANAALE--GTLPLTIP--GDVEQAMKTLQTFPGIGRW------------------ 218 (283)
T ss_pred HcCC-HHHHHHCCCCHHHHHHHHHHHHHHHc--CCCCcccc--CCHHHHHHHHhcCCCcCHH------------------
Confidence 9986 56799999986 89999999999998 77776653 4679999999999999999
Q ss_pred cchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCcccc-chhHHHHHH
Q psy4725 278 YLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPV-DTHVYQIAC 356 (457)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~Pv-D~~v~~~a~ 356 (457)
|||||+||+|+++++||. |+|+.|.+.
T Consensus 219 ----------------------------------------------------TA~~vllr~lg~~D~fp~~D~~l~~~~~ 246 (283)
T PRK10308 219 ----------------------------------------------------TANYFALRGWQAKDVFLPDDYLIKQRFP 246 (283)
T ss_pred ----------------------------------------------------HHHHHHHHhCCCCCCCCcccHHHHHhcc
Confidence 999999999999999965 999987431
Q ss_pred hhcccCCCCCCCCCHHHHHHHHHHHHhhhcCcHHHHHHHHHhccc
Q psy4725 357 NHYHFQKSTSKTLTPAVYNQIRAFFADKFGKYAGWAHSILFCADL 401 (457)
Q Consensus 357 ~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~~ag~A~~~lf~~~l 401 (457)
..++ +++.++ .+.|+||+|||..|||+...
T Consensus 247 -----------~~~~---~~~~~~-a~~w~P~rsya~~~LW~~~~ 276 (283)
T PRK10308 247 -----------GMTP---AQIRRY-AERWKPWRSYALLHIWYTEG 276 (283)
T ss_pred -----------cCCH---HHHHHH-HHhcCCHHHHHHHHHHHcCC
Confidence 1233 566665 45799999999999998843
No 5
>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=99.96 E-value=6.5e-29 Score=215.59 Aligned_cols=113 Identities=34% Similarity=0.667 Sum_probs=89.9
Q ss_pred ccccCCcccccccccccccccceeecCCCCcccCCeEEEEECCeEEEEEEcCCeEEEEEEe----CCCCCHHHHHHHHHH
Q psy4725 13 KILCPAIELSLTLTLLGGQSFRWKQLTSDEKKLGNRFQGVFKECVWTLWADPSYLHYQVFS----QHKLNANSVETMLKE 88 (457)
Q Consensus 13 ~l~~~~~~l~L~~tL~~GQ~FrW~~~~~~~~~~~~~~~gv~~~~v~~l~q~~~~L~y~~~~----~~~~~~~~~~~~lr~ 88 (457)
+|++++.+|||+.||+|||||||++.+ +..|.||++++||.|+|+++.+.|+++. ......++..+.|++
T Consensus 1 ~l~~~~~~~~L~~tL~sGQ~FrW~~~~------~~~~~gv~~~~~~~l~q~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 74 (117)
T PF07934_consen 1 KLPIPKEEFNLDKTLFSGQSFRWRKID------DGEWSGVIGDRVVQLRQDDDNLLYRCLSSAEPSNSSSEEDIEEFLRD 74 (117)
T ss_dssp EEE-STTT--HHHHCCTTS-SSEEEEC------TTEEEEEETTEEEEEEEETTEEEEECE--TTS---S-HHHHHHCHHH
T ss_pred CCcCCHHHcCHHHHhcccCcccCEEeC------CCeEEEEcCCeEEEEEECCCEEEEEEecCCCcccccchhhHHHHHHH
Confidence 578999999999999999999999997 4569999999999999999999999876 223356788999999
Q ss_pred hhcCCCCHHHHHHHHhccChhHHHhhhhhCCccccCCCHHHHH
Q psy4725 89 YFRLDENLPELYAEWSNRDAFFRQTCGDFVGIRMLNQDLTENI 131 (457)
Q Consensus 89 YFdLD~DL~~l~~~~~~~Dp~L~~li~~~~GLRILrqDPfE~L 131 (457)
||+||+||+++|+.|+..||.|+.+++.++|||||||||||||
T Consensus 75 YF~Ld~dl~~l~~~~~~~D~~l~~~~~~~~GlRiLrQdp~E~L 117 (117)
T PF07934_consen 75 YFDLDVDLEKLYEDWSKKDPRLAKAIDKYRGLRILRQDPFETL 117 (117)
T ss_dssp HTTTTS-HHHHHHHHCCHSHHHHHHHHCTTT-------HHHHH
T ss_pred HhcCCccHHHHHHHHhhhCHHHHHHHhcCCCcEEECCChhhhC
Confidence 9999999999999998889999999999999999999999997
No 6
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.93 E-value=5.7e-26 Score=204.41 Aligned_cols=152 Identities=30% Similarity=0.422 Sum_probs=130.3
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChHHHH
Q psy4725 128 TENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVEAKL 207 (457)
Q Consensus 128 fE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~Ee~L 207 (457)
||+|+++||+||++++++.+++++|++.|| |||++|+.++ +++|
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g-----------------------------------pt~~~l~~~~-~~~l 44 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG-----------------------------------PTPEALAAAD-EEEL 44 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC-----------------------------------CCHHHHHCCC-HHHH
Confidence 799999999999999999999999999875 6899999986 5679
Q ss_pred HhcCCc----hhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccchhhh
Q psy4725 208 RQLGFG----YRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQV 283 (457)
Q Consensus 208 R~~g~g----YRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~~ 283 (457)
+.+|.+ +||++|+++|+.+.+..+. +.. +++++++.|++|||||||
T Consensus 45 ~~~~~~~G~~~kA~~i~~~a~~~~~~~~~--~~~----~~~~~~~~L~~l~GIG~~------------------------ 94 (158)
T cd00056 45 RELIRSLGYRRKAKYLKELARAIVEGFGG--LVL----DDPDAREELLALPGVGRK------------------------ 94 (158)
T ss_pred HHHHHhcChHHHHHHHHHHHHHHHHHcCC--ccC----CCcccHHHHHcCCCCCHH------------------------
Confidence 988776 7899999999999994332 221 678999999999999999
Q ss_pred hhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhcccCC
Q psy4725 284 YSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQK 363 (457)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~~~~ 363 (457)
||||+++|+++ .++||+|+|+.|++.+.|....
T Consensus 95 ----------------------------------------------tA~~~l~~~~~-~~~~pvD~~v~r~~~~~~~~~~ 127 (158)
T cd00056 95 ----------------------------------------------TANVVLLFALG-PDAFPVDTHVRRVLKRLGLIPK 127 (158)
T ss_pred ----------------------------------------------HHHHHHHHHCC-CCCCccchhHHHHHHHhCCCCC
Confidence 99999999999 8999999999999999986321
Q ss_pred CCCCCCCHHHHHHHHHHHHhhh-cCcHHHHHHHHHhc
Q psy4725 364 STSKTLTPAVYNQIRAFFADKF-GKYAGWAHSILFCA 399 (457)
Q Consensus 364 ~~~~~lt~~~y~~i~~~~~~~f-g~~ag~A~~~lf~~ 399 (457)
+..|+++++++...+ ++|+++++.+||..
T Consensus 128 -------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 157 (158)
T cd00056 128 -------KKTPEELEELLEELLPKPYWGEANQALMDL 157 (158)
T ss_pred -------CCCHHHHHHHHHHHCCHHHHHHHHHHHHHc
Confidence 123678888877766 48999999999864
No 7
>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=99.91 E-value=7.3e-24 Score=198.82 Aligned_cols=159 Identities=19% Similarity=0.299 Sum_probs=124.1
Q ss_pred hHHHhhhhhCCccc--cCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcc
Q psy4725 109 FFRQTCGDFVGIRM--LNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAV 186 (457)
Q Consensus 109 ~L~~li~~~~GLRI--LrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~ 186 (457)
.+..+.+.+++.+. ..+||||+||++|+|||++++.+.++..+|.+
T Consensus 6 i~~~l~~~~~~~~~~~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~-------------------------------- 53 (191)
T TIGR01083 6 ILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLFE-------------------------------- 53 (191)
T ss_pred HHHHHHHHCCCCCcccCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHH--------------------------------
Confidence 34455566776653 46899999999999999999999999887743
Q ss_pred cccccCCcHHHHcCCChHHHH----HhcCCc-hhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCC
Q psy4725 187 TKFFAFPSIDALARPAVEAKL----RQLGFG-YRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVG 261 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~L----R~~g~g-YRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a 261 (457)
.||||++|++++. ++| |.+||. .||+||+++|+++.+..| .+.++.++.|++|||||+|
T Consensus 54 ----~~pt~~~l~~~~~-~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~---------~~~~~~~~~L~~l~GIG~k-- 117 (191)
T TIGR01083 54 ----VYPTPQALAQAGL-EELEEYIKSIGLYRNKAKNIIALCRILVERYG---------GEVPEDREELVKLPGVGRK-- 117 (191)
T ss_pred ----HCCCHHHHHcCCH-HHHHHHHHhcCChHHHHHHHHHHHHHHHHHcC---------CCCchHHHHHHhCCCCcHH--
Confidence 3689999999864 455 778884 589999999999988422 1245679999999999999
Q ss_pred CcccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCC
Q psy4725 262 DGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSH 341 (457)
Q Consensus 262 ~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~ 341 (457)
|||||++|++++
T Consensus 118 --------------------------------------------------------------------tA~~ill~~~~~ 129 (191)
T TIGR01083 118 --------------------------------------------------------------------TANVVLNVAFGI 129 (191)
T ss_pred --------------------------------------------------------------------HHHHHHHHHcCC
Confidence 999999999999
Q ss_pred CCccccchhHHHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhhcCcHHHHH
Q psy4725 342 LQAVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFGKYAGWAH 393 (457)
Q Consensus 342 ~~~~PvD~~v~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~~ag~A~ 393 (457)
+ .||||+||.|++.|++.... +.|++++.++.+.+ |+..|+.
T Consensus 130 ~-~~~vD~~v~Ri~~r~g~~~~--------~~~~~~~~~l~~~~-p~~~~~~ 171 (191)
T TIGR01083 130 P-AIAVDTHVFRVSNRLGLSKG--------KDPDKVEEELLKLI-PREFWTK 171 (191)
T ss_pred C-ccccchhHHHHHHHcCCCCC--------CCHHHHHHHHHHHC-CchhHHH
Confidence 6 59999999999999876421 12567777666554 4444443
No 8
>PRK10702 endonuclease III; Provisional
Probab=99.90 E-value=3.2e-23 Score=198.52 Aligned_cols=141 Identities=16% Similarity=0.239 Sum_probs=114.3
Q ss_pred ccCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCC
Q psy4725 122 MLNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARP 201 (457)
Q Consensus 122 ILrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~ 201 (457)
...+||||+||++|||||+++.++.+.+.+|- ..||||++|+++
T Consensus 24 ~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~------------------------------------~~~pt~e~l~~a 67 (211)
T PRK10702 24 LNFSSPFELLIAVLLSAQATDVSVNKATAKLY------------------------------------PVANTPAAMLEL 67 (211)
T ss_pred CCCCChHHHHHHHHHHhhcCHHHHHHHHHHHH------------------------------------HHcCCHHHHHCC
Confidence 35689999999999999999999999988763 247999999998
Q ss_pred ChHHHHHh----cCCc-hhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCC
Q psy4725 202 AVEAKLRQ----LGFG-YRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADP 276 (457)
Q Consensus 202 ~~Ee~LR~----~g~g-YRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~ 276 (457)
+. ++|+. +||. .||++|+++|+.+.+..|. +.+++++.|++|||||+|
T Consensus 68 ~~-~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~---------~~p~~~~~Ll~lpGVG~k----------------- 120 (211)
T PRK10702 68 GV-EGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG---------EVPEDRAALEALPGVGRK----------------- 120 (211)
T ss_pred CH-HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCC---------CCCchHHHHhcCCcccHH-----------------
Confidence 64 45654 5553 3899999999999874321 356789999999999999
Q ss_pred ccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHH
Q psy4725 277 SYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIAC 356 (457)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~ 356 (457)
|||||++|++++ .+|||||||.||+.
T Consensus 121 -----------------------------------------------------tA~~ill~a~~~-~~~~VDt~v~Rv~~ 146 (211)
T PRK10702 121 -----------------------------------------------------TANVVLNTAFGW-PTIAVDTHIFRVCN 146 (211)
T ss_pred -----------------------------------------------------HHHHHHHHHcCC-CcccccchHHHHHH
Confidence 999999999999 69999999999999
Q ss_pred hhcccCCCCCCCCCHHHHHHHHHHHHhhhcC
Q psy4725 357 NHYHFQKSTSKTLTPAVYNQIRAFFADKFGK 387 (457)
Q Consensus 357 ~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~ 387 (457)
|.|.... +.|++++..+.+.+.+
T Consensus 147 r~g~~~~--------~~~~~~~~~l~~~lp~ 169 (211)
T PRK10702 147 RTQFAPG--------KNVEQVEEKLLKVVPA 169 (211)
T ss_pred HhCCCCC--------CCHHHHHHHHHHhCCc
Confidence 9986431 1256777776666644
No 9
>KOG1918|consensus
Probab=99.87 E-value=8.8e-22 Score=188.76 Aligned_cols=188 Identities=18% Similarity=0.230 Sum_probs=157.4
Q ss_pred HHHhccChhHHHhhhhhCCccc-cCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCC
Q psy4725 101 AEWSNRDAFFRQTCGDFVGIRM-LNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSH 179 (457)
Q Consensus 101 ~~~~~~Dp~L~~li~~~~GLRI-LrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~ 179 (457)
.++.+.||.|..++..+..++. -.|.|||.|+++|+|||.+.+++..+.+|++..||..
T Consensus 48 ~hl~~kd~~L~~lv~~~~p~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~-------------------- 107 (254)
T KOG1918|consen 48 SHLDEKDPSLVKLVGNHEPLTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGA-------------------- 107 (254)
T ss_pred HhhhhcchHHHHHhcCCCCCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC--------------------
Confidence 4455789999999998887776 5789999999999999999999999999999999831
Q ss_pred CCCCCcccccccCCcHHHHcCCChHHHHHhcCCchh-HHHHHHHHHHHHHcCC-CCcchhhcCCCHHHHHHHhhcCCCcc
Q psy4725 180 AKSCPAVTKFFAFPSIDALARPAVEAKLRQLGFGYR-AKFIQKSAEYIIQGGG-ESWLERLGGKSYEEAREELQRLPGIG 257 (457)
Q Consensus 180 ~~~~p~~~~~ysFPTpe~LA~~~~Ee~LR~~g~gYR-AkyI~~~A~~~~e~~G-~~~l~~l~~~~~~eare~L~~LpGVG 257 (457)
+.||+|+.+..++. ++||+|||+-| +.||+.+|++..+ | -.....+..++.|+..+.|+.++|||
T Consensus 108 ----------~~~~~pe~i~~~~~-~~lrkcG~S~rK~~yLh~lA~~~~n--g~I~s~~~i~~mseEeL~~~LT~VKGIg 174 (254)
T KOG1918|consen 108 ----------EKFPTPEFIDPLDC-EELRKCGFSKRKASYLHSLAEAYTN--GYIPSKSGIEKMSEEELIERLTNVKGIG 174 (254)
T ss_pred ----------cCCCCchhcCcCCH-HHHHHhCcchhhHHHHHHHHHHHhc--CCCCchHHHhhcCHHHHHHHHHhccCcc
Confidence 46899999999875 57999999765 9999999999998 6 33445567899999999999999999
Q ss_pred ccCCCcccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHH
Q psy4725 258 AKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLM 337 (457)
Q Consensus 258 pK~a~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~ 337 (457)
+| ++.+.++|
T Consensus 175 ~W----------------------------------------------------------------------tv~MflIf 184 (254)
T KOG1918|consen 175 RW----------------------------------------------------------------------TVEMFLIF 184 (254)
T ss_pred ce----------------------------------------------------------------------eeeeeeee
Confidence 99 99999999
Q ss_pred hcCCCCcccc-chhHHHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhhcCcHHHHHHHHHhc
Q psy4725 338 SLSHLQAVPV-DTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFGKYAGWAHSILFCA 399 (457)
Q Consensus 338 ~l~~~~~~Pv-D~~v~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~~ag~A~~~lf~~ 399 (457)
||+|+|++|+ |..|++-+...|... .-+.|. ++. ...+.|.||+.-|.+|||.-
T Consensus 185 sL~R~DVmp~dDlgir~g~k~l~gl~----~~p~~~---eve-kl~e~~kpyRtvaawYlWki 239 (254)
T KOG1918|consen 185 SLHRPDVMPADDLGIRNGVKKLLGLK----PLPLPK---EVE-KLCEKCKPYRTVAAWYLWKI 239 (254)
T ss_pred ccCCCcccCchhhhHHHHHHHHhCCC----CCCchH---HHH-HHhhhccchHHHHHHHHHhh
Confidence 9999999999 678888887665422 113332 232 35789999999999999963
No 10
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.87 E-value=3.1e-21 Score=185.14 Aligned_cols=170 Identities=19% Similarity=0.284 Sum_probs=132.3
Q ss_pred HHHhhhhhCCccc-cC-CCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCccc
Q psy4725 110 FRQTCGDFVGIRM-LN-QDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVT 187 (457)
Q Consensus 110 L~~li~~~~GLRI-Lr-qDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~ 187 (457)
+..+...++..+. +. .||||.||+.|+|||++..+..+...+|-+.
T Consensus 10 ~~~l~~~~p~~~~~l~~~~pf~lLva~iLSaqttD~~vn~at~~Lf~~-------------------------------- 57 (211)
T COG0177 10 LDRLRELYPEPKTELDFKDPFELLVAVILSAQTTDEVVNKATPALFKR-------------------------------- 57 (211)
T ss_pred HHHHHHHCCCCCCccCcCCcHHHHHHHHHhccCchHHHHHHHHHHHHH--------------------------------
Confidence 4444555666554 44 8999999999999999999999999887665
Q ss_pred ccccCCcHHHHcCCCh---HHHHHhcCCch-hHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCc
Q psy4725 188 KFFAFPSIDALARPAV---EAKLRQLGFGY-RAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDG 263 (457)
Q Consensus 188 ~~ysFPTpe~LA~~~~---Ee~LR~~g~gY-RAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~ 263 (457)
||||++|++++. ++.|+..||.. +|++|+++|+.|.+..|. ..++.+++|++|||||+|
T Consensus 58 ----~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g---------~vP~~~~eL~~LPGVGrK---- 120 (211)
T COG0177 58 ----YPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG---------EVPDTREELLSLPGVGRK---- 120 (211)
T ss_pred ----cCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC---------CCCchHHHHHhCCCcchH----
Confidence 468999998763 34567889964 599999999999996432 367889999999999999
Q ss_pred ccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCC
Q psy4725 264 VFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQ 343 (457)
Q Consensus 264 vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~ 343 (457)
||++|+.++++.+
T Consensus 121 ------------------------------------------------------------------TAnvVL~~a~g~p- 133 (211)
T COG0177 121 ------------------------------------------------------------------TANVVLSFAFGIP- 133 (211)
T ss_pred ------------------------------------------------------------------HHHHHHHhhcCCC-
Confidence 9999999999999
Q ss_pred ccccchhHHHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhhcC--cHHHHHHHHHhccccc
Q psy4725 344 AVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFGK--YAGWAHSILFCADLKK 403 (457)
Q Consensus 344 ~~PvD~~v~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~--~ag~A~~~lf~~~l~~ 403 (457)
++||||||.||+.|+..... -+ +.++...+.+.+.+ |--..+..+++.+.-.
T Consensus 134 ~i~VDTHV~Rvs~R~gl~~~-----~~---p~~ve~~L~~~iP~~~~~~~h~~lI~~GR~iC 187 (211)
T COG0177 134 AIAVDTHVHRVSNRLGLVPG-----KT---PEEVEEALMKLIPKELWTDLHHWLILHGRYIC 187 (211)
T ss_pred cccccchHHHHHHHhCCCCC-----CC---HHHHHHHHHHHCCHHHHHHHHHHHHHhhhhhc
Confidence 99999999999999987542 12 36777777777754 4444555555554433
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=99.87 E-value=1.7e-21 Score=174.15 Aligned_cols=141 Identities=24% Similarity=0.406 Sum_probs=115.2
Q ss_pred HhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChHHHH----HhcC
Q psy4725 136 CSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVEAKL----RQLG 211 (457)
Q Consensus 136 cSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~Ee~L----R~~g 211 (457)
+|||++++.+.+++++|++.| |||++|++++. ++| +.+|
T Consensus 1 l~qq~~~~~a~~~~~~l~~~~------------------------------------~~~~~l~~~~~-~eL~~~l~~~g 43 (149)
T smart00478 1 LSQQTSDEAVNKATERLFEKF------------------------------------PTPEDLAAADE-EELEELIRPLG 43 (149)
T ss_pred CCCcccHHHHHHHHHHHHHHC------------------------------------CCHHHHHCCCH-HHHHHHHHHcC
Confidence 589999999999999998764 67899988764 344 8889
Q ss_pred Cc-hhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccchhhhhhccccc
Q psy4725 212 FG-YRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLN 290 (457)
Q Consensus 212 ~g-YRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~~~~~~~~~ 290 (457)
|. .||+||+++|+.+.+..+ .+.+++++.|++|||||||
T Consensus 44 ~~~~ka~~i~~~a~~~~~~~~---------~~~~~~~~~L~~l~GIG~~------------------------------- 83 (149)
T smart00478 44 FYRRKAKYLIELARILVEEYG---------GEVPDDREELLKLPGVGRK------------------------------- 83 (149)
T ss_pred ChHHHHHHHHHHHHHHHHHHC---------CCccHHHHHHHcCCCCcHH-------------------------------
Confidence 86 479999999999987311 1134688999999999999
Q ss_pred cchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhcccCCCCCCCCC
Q psy4725 291 TNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQKSTSKTLT 370 (457)
Q Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~~~~~~~~~lt 370 (457)
+|||+++|++++ ..+|+|+||.|++.+.|....
T Consensus 84 ---------------------------------------tA~~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~~------- 116 (149)
T smart00478 84 ---------------------------------------TANAVLSFALGK-PFIPVDTHVLRIAKRLGLVDK------- 116 (149)
T ss_pred ---------------------------------------HHHHHHHHHCCC-CCCccchHHHHHHHHhCCCCC-------
Confidence 999999999999 889999999999999886431
Q ss_pred HHHHHHHHHHHHhhhcC--cHHHHHHHHHhcc
Q psy4725 371 PAVYNQIRAFFADKFGK--YAGWAHSILFCAD 400 (457)
Q Consensus 371 ~~~y~~i~~~~~~~fg~--~ag~A~~~lf~~~ 400 (457)
+..|+.++..+.+.+++ |+++++.|||+..
T Consensus 117 ~~~~~~~~~~~~~~~p~~~~~~~~~~~l~~g~ 148 (149)
T smart00478 117 KSTPEEVEKLLEKLLPKEDWRELNLLLIDFGR 148 (149)
T ss_pred CCCHHHHHHHHHHHCCHHHHHHHHHHHHHHcC
Confidence 22467888777666543 9999999999864
No 12
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.85 E-value=1.5e-20 Score=181.23 Aligned_cols=148 Identities=20% Similarity=0.204 Sum_probs=119.6
Q ss_pred cCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCC
Q psy4725 123 LNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPA 202 (457)
Q Consensus 123 LrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~ 202 (457)
.+.+|||+||+.|+|||+++.+..+.+.+|.+++.- ++ ..||||++|++++
T Consensus 26 p~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~-----~~------------------------~~~~t~e~L~~a~ 76 (218)
T PRK13913 26 PNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFIL-----EN------------------------DDEINLKKIAYIE 76 (218)
T ss_pred cCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhccc-----cc------------------------ccCCCHHHHHcCC
Confidence 357899999999999999999999999999876420 01 2469999999986
Q ss_pred hHHHHHhc----CCch-hHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCc
Q psy4725 203 VEAKLRQL----GFGY-RAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPS 277 (457)
Q Consensus 203 ~Ee~LR~~----g~gY-RAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~ 277 (457)
+++|+++ ||.. ||+||+++|+.+.+..|. ++. +..++.++.|+++||||+|
T Consensus 77 -~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~--~~~---~~~~~~re~Ll~l~GIG~k------------------ 132 (218)
T PRK13913 77 -FSKLAECVRPSGFYNQKAKRLIDLSENILKDFGS--FEN---FKQEVTREWLLDQKGIGKE------------------ 132 (218)
T ss_pred -HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCC--chh---ccCchHHHHHHcCCCccHH------------------
Confidence 4566665 9854 699999999999885432 222 2335789999999999999
Q ss_pred cchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHh
Q psy4725 278 YLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACN 357 (457)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~ 357 (457)
|||||++|+++++ +||||+|++||+.|
T Consensus 133 ----------------------------------------------------TAd~iLlya~~rp-~fvVDty~~Rv~~R 159 (218)
T PRK13913 133 ----------------------------------------------------SADAILCYVCAKE-VMVVDKYSYLFLKK 159 (218)
T ss_pred ----------------------------------------------------HHHHHHHHHcCCC-ccccchhHHHHHHH
Confidence 9999999999995 89999999999999
Q ss_pred hcccCCCCCCCCCHHHHHHHHHHHHhhh
Q psy4725 358 HYHFQKSTSKTLTPAVYNQIRAFFADKF 385 (457)
Q Consensus 358 ~y~~~~~~~~~lt~~~y~~i~~~~~~~f 385 (457)
.... ++.|+++++++.+.+
T Consensus 160 lG~~---------~~~y~~~~~~~~~~l 178 (218)
T PRK13913 160 LGIE---------IEDYDELQHFFEKGV 178 (218)
T ss_pred cCCC---------CCCHHHHHHHHHHhh
Confidence 7542 124899999988755
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=99.84 E-value=3.5e-20 Score=184.04 Aligned_cols=158 Identities=18% Similarity=0.297 Sum_probs=119.6
Q ss_pred CCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCCh
Q psy4725 124 NQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAV 203 (457)
Q Consensus 124 rqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~ 203 (457)
.+|||+++|+.|++||++++++.....+|.+ .||||++|++++
T Consensus 23 ~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~------------------------------------~fpt~~~La~a~- 65 (275)
T TIGR01084 23 NKTPYRVWLSEVMLQQTQVATVIPYFERFLE------------------------------------RFPTVQALANAP- 65 (275)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHHH------------------------------------hCCCHHHHHCcC-
Confidence 5799999999999999999999999988754 369999999986
Q ss_pred HHHH----HhcCCchhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccc
Q psy4725 204 EAKL----RQLGFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYL 279 (457)
Q Consensus 204 Ee~L----R~~g~gYRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~ 279 (457)
+++| +.+|+..||++|+++|+.|.+..|. ..++.++.|++|||||+|
T Consensus 66 ~eeL~~~~~~lG~y~RAr~L~~~A~~i~~~~~g---------~~p~~~~~L~~LpGIG~~-------------------- 116 (275)
T TIGR01084 66 QDEVLKLWEGLGYYARARNLHKAAQEVVEEFGG---------EFPQDFEDLAALPGVGRY-------------------- 116 (275)
T ss_pred HHHHHHHHHHCCcHHHHHHHHHHHHHHHHHcCC---------CCcHHHHHHHhCCCCCHH--------------------
Confidence 5567 5566655899999999999885322 134678999999999999
Q ss_pred hhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhc
Q psy4725 280 HYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHY 359 (457)
Q Consensus 280 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y 359 (457)
|||||++|+++++. ++||+||.|++.|.|
T Consensus 117 --------------------------------------------------TA~~Il~~a~~~~~-~~vD~~v~RVl~Rl~ 145 (275)
T TIGR01084 117 --------------------------------------------------TAGAILSFALNKPY-PILDGNVKRVLSRLF 145 (275)
T ss_pred --------------------------------------------------HHHHHHHHHCCCCC-CcchHhHHHHHHHHc
Confidence 99999999999985 459999999999998
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHhhhcC--cHHHHHHHHHhccc
Q psy4725 360 HFQKSTSKTLTPAVYNQIRAFFADKFGK--YAGWAHSILFCADL 401 (457)
Q Consensus 360 ~~~~~~~~~lt~~~y~~i~~~~~~~fg~--~ag~A~~~lf~~~l 401 (457)
..... ...+.....+.+.+.+.+.+ +.-|.|.++.....
T Consensus 146 ~~~~~---~~~~~~~~~l~~~~~~~lp~~~~~~~n~alm~lG~~ 186 (275)
T TIGR01084 146 AVEGW---PGKKKVENRLWTLAESLLPKADPEAFNQALMDLGAM 186 (275)
T ss_pred cCcCC---CCHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHhHH
Confidence 64321 11234455555445554432 44455665555433
No 14
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.80 E-value=9.3e-19 Score=179.12 Aligned_cols=156 Identities=19% Similarity=0.290 Sum_probs=116.6
Q ss_pred CCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCCh
Q psy4725 124 NQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAV 203 (457)
Q Consensus 124 rqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~ 203 (457)
..|||+.+||.|++||+++..+....++|.++ |||+++|++++
T Consensus 27 ~~dpy~ilVseILlQQT~v~~v~~~~~rl~~~------------------------------------fPt~~~La~a~- 69 (350)
T PRK10880 27 DKTPYKVWLSEVMLQQTQVATVIPYFERFMAR------------------------------------FPTVTDLANAP- 69 (350)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHHHH------------------------------------CcCHHHHHCcC-
Confidence 46999999999999999999999999888663 68999999986
Q ss_pred HHHHHh--cCCch--hHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccc
Q psy4725 204 EAKLRQ--LGFGY--RAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYL 279 (457)
Q Consensus 204 Ee~LR~--~g~gY--RAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~ 279 (457)
+++|.+ .|+|| ||+||+++|+.|.+..|. ..++.++.|++|||||+|
T Consensus 70 ~eel~~~~~glGyy~RAr~L~~~A~~i~~~~~g---------~~p~~~~~L~~LpGIG~~-------------------- 120 (350)
T PRK10880 70 LDEVLHLWTGLGYYARARNLHKAAQQVATLHGG---------EFPETFEEVAALPGVGRS-------------------- 120 (350)
T ss_pred HHHHHHHHHcCChHHHHHHHHHHHHHHHHHhCC---------CchhhHHHHhcCCCccHH--------------------
Confidence 456665 37776 999999999999874321 246789999999999999
Q ss_pred hhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhc
Q psy4725 280 HYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHY 359 (457)
Q Consensus 280 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y 359 (457)
|||||++|++++. .++||+||+||+.|.|
T Consensus 121 --------------------------------------------------TA~aIl~~af~~~-~~iVD~nV~RV~~Rl~ 149 (350)
T PRK10880 121 --------------------------------------------------TAGAILSLSLGKH-FPILDGNVKRVLARCY 149 (350)
T ss_pred --------------------------------------------------HHHHHHHHHCCCC-eecccHHHHHHHHHHh
Confidence 9999999999984 3446999999999988
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHhhhc--CcHHHHHHHHHhc
Q psy4725 360 HFQKSTSKTLTPAVYNQIRAFFADKFG--KYAGWAHSILFCA 399 (457)
Q Consensus 360 ~~~~~~~~~lt~~~y~~i~~~~~~~fg--~~ag~A~~~lf~~ 399 (457)
...... ..++..+.+.++..+.+. .+..+.|.++-+.
T Consensus 150 ~i~~~~---~~~~~~~~l~~~~~~l~p~~~~~~~nqalm~lG 188 (350)
T PRK10880 150 AVSGWP---GKKEVENRLWQLSEQVTPAVGVERFNQAMMDLG 188 (350)
T ss_pred cccCCC---ChHHHHHHHHHHHHHhCChhHHHHHHHHHHHhh
Confidence 643211 122333444444333332 2444566555544
No 15
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.74 E-value=1.7e-17 Score=159.28 Aligned_cols=161 Identities=20% Similarity=0.248 Sum_probs=121.9
Q ss_pred cCCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCC
Q psy4725 123 LNQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPA 202 (457)
Q Consensus 123 LrqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~ 202 (457)
-..|||+.|++.|+|||+++....++..+|... .+ -.++++|
T Consensus 33 ~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~~~--------------------------------~l--~~~~eeL---- 74 (208)
T PRK01229 33 DEEDLFSELSFCILTANSSAEGGIKAQKEIGDG--------------------------------FL--YLSEEEL---- 74 (208)
T ss_pred ccCChHHHHHHHHhcCcCcHHHHHHHHHhcCHH--------------------------------Hc--CCCHHHH----
Confidence 346899999999999999999999999988321 11 1245555
Q ss_pred hHHHHHhcCCch---hHHHHHHHHHHHHHcCCCCcchhh--cCCCHHHHHHHhh-cCCCccccCCCcccccccccccCCC
Q psy4725 203 VEAKLRQLGFGY---RAKFIQKSAEYIIQGGGESWLERL--GGKSYEEAREELQ-RLPGIGAKVGDGVFKEHVWTLWADP 276 (457)
Q Consensus 203 ~Ee~LR~~g~gY---RAkyI~~~A~~~~e~~G~~~l~~l--~~~~~~eare~L~-~LpGVGpK~a~~vl~~~~~~~~~~~ 276 (457)
++.||.+|.|| ||+||+++++.+. . +..+ ...+.+++++.|+ ++||||+|
T Consensus 75 -~~~Ir~~Gygf~~~KAk~I~~~~~~~~----~--l~~~~~~~~~~~~~R~~Ll~~lpGIG~K----------------- 130 (208)
T PRK01229 75 -EEKLKEVGHRFYNKRAEYIVEARKLYG----K--LKEIIKADKDQFEAREFLVKNIKGIGYK----------------- 130 (208)
T ss_pred -HHHHHHhhcccHHHHHHHHHHHHHHHH----H--HHHHHhccCCchHHHHHHHHcCCCCcHH-----------------
Confidence 35789997443 6999999998751 1 1222 2445689999999 99999999
Q ss_pred ccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHH
Q psy4725 277 SYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIAC 356 (457)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~ 356 (457)
+||||++.... .++|||||||.|++.
T Consensus 131 -----------------------------------------------------TAd~vL~~~~~-~~~~iVDtHv~Ri~~ 156 (208)
T PRK01229 131 -----------------------------------------------------EASHFLRNVGY-EDLAILDRHILRFLK 156 (208)
T ss_pred -----------------------------------------------------HHHHHHHHccC-CCeeeeeHHHHHHHH
Confidence 99999975444 679999999999999
Q ss_pred hhcccCCCCCCCCCHHHHHHHHHHHH---hhhcCcHHHHHHHHHhcc
Q psy4725 357 NHYHFQKSTSKTLTPAVYNQIRAFFA---DKFGKYAGWAHSILFCAD 400 (457)
Q Consensus 357 ~~y~~~~~~~~~lt~~~y~~i~~~~~---~~fg~~ag~A~~~lf~~~ 400 (457)
|++..... .+++|++.|.++...+. ..+|-++|---.|+|+..
T Consensus 157 RlG~~~~~-~~~lt~~~y~~~E~~l~~~~~~~~~~~~~Ldl~~w~~~ 202 (208)
T PRK01229 157 RYGLIEEI-PKTLSKKRYLEIEEILREIAEELGISLGELDLYIWYKE 202 (208)
T ss_pred HhCCCccc-ccccCcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 99875432 23677888888877654 456778898889999864
No 16
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.62 E-value=3.6e-15 Score=149.44 Aligned_cols=90 Identities=29% Similarity=0.464 Sum_probs=74.0
Q ss_pred cCCcHHHHcCCChHHHHHh--cCCch--hHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccc
Q psy4725 191 AFPSIDALARPAVEAKLRQ--LGFGY--RAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 191 sFPTpe~LA~~~~Ee~LR~--~g~gY--RAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
.|||+++|++++ +++|.+ -|+|| ||++|+++|+.|.++.+. . .++.++.|++|||||+|
T Consensus 21 ~fPt~e~La~a~-~~el~~~~~glGyy~RAr~L~~~A~~i~~~~~g-------~--~P~~~~~L~~LpGIG~k------- 83 (289)
T PRK13910 21 AFPTLKDLANAP-LEEVLLLWRGLGYYSRAKNLKKSAEICVKEHHS-------Q--LPNDYQSLLKLPGIGAY------- 83 (289)
T ss_pred HCCCHHHHHCCC-HHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCC-------C--CChhHHHHHhCCCCCHH-------
Confidence 589999999986 455654 26665 999999999999875321 1 23458999999999999
Q ss_pred cccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccc
Q psy4725 267 EHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVP 346 (457)
Q Consensus 267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~P 346 (457)
|||||++|+++++ .+|
T Consensus 84 ---------------------------------------------------------------TA~aIl~~af~~~-~~~ 99 (289)
T PRK13910 84 ---------------------------------------------------------------TANAILCFGFREK-SAC 99 (289)
T ss_pred ---------------------------------------------------------------HHHHHHHHHCCCC-cCc
Confidence 9999999999986 569
Q ss_pred cchhHHHHHHhhccc
Q psy4725 347 VDTHVYQIACNHYHF 361 (457)
Q Consensus 347 vD~~v~~~a~~~y~~ 361 (457)
||+||+||+.|.|..
T Consensus 100 VD~nV~RVl~Rl~g~ 114 (289)
T PRK13910 100 VDANIKRVLLRLFGL 114 (289)
T ss_pred ccHHHHHHHHHHhcC
Confidence 999999999998754
No 17
>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=99.48 E-value=3.1e-13 Score=114.61 Aligned_cols=61 Identities=33% Similarity=0.584 Sum_probs=54.6
Q ss_pred HHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChHHHHHhc-
Q psy4725 132 FSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVEAKLRQL- 210 (457)
Q Consensus 132 IsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~Ee~LR~~- 210 (457)
|++|||||++++++.+++.+|+++|| ||||++|+.++ +++|+.+
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g----------------------------------~pt~~~l~~~~-~~el~~~i 45 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYG----------------------------------FPTPEALAEAS-EEELRELI 45 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHS----------------------------------CSSHHHHHCSH-HHHHHHHH
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhc----------------------------------CCCHHHHHhCC-HHHHHHHh
Confidence 68999999999999999999999986 58999999975 6678877
Q ss_pred ---CCc-hhHHHHHHHHHHHH
Q psy4725 211 ---GFG-YRAKFIQKSAEYII 227 (457)
Q Consensus 211 ---g~g-YRAkyI~~~A~~~~ 227 (457)
||+ +||+||+++|+.+.
T Consensus 46 ~~~G~~~~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 46 RPLGFSRRKAKYIIELARAIL 66 (108)
T ss_dssp TTSTSHHHHHHHHHHHHHHHH
T ss_pred hccCCCHHHHHHHHHHHHHhh
Confidence 998 89999999999886
No 18
>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=99.47 E-value=4.5e-13 Score=126.00 Aligned_cols=101 Identities=19% Similarity=0.207 Sum_probs=80.2
Q ss_pred CCCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCCh
Q psy4725 124 NQDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAV 203 (457)
Q Consensus 124 rqDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~ 203 (457)
..+|||.||+.|+|||+++.++.+.+.+|.+.+|. +||++|++++.
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~----------------------------------~tp~~La~a~~ 60 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGS----------------------------------LDAEDIAKYDP 60 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCC----------------------------------CCHHHHHcCCH
Confidence 46899999999999999999999999999887762 57999998864
Q ss_pred H---HHHHhc----CCc-hhHHHHHHHHHHHHHcCCCCcchhhcC---CCHHHHHHHhhcCCCcccc
Q psy4725 204 E---AKLRQL----GFG-YRAKFIQKSAEYIIQGGGESWLERLGG---KSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 204 E---e~LR~~----g~g-YRAkyI~~~A~~~~e~~G~~~l~~l~~---~~~~eare~L~~LpGVGpK 259 (457)
+ +.|+.. ||. .+|++|+++|+.|.+..|. .+..|.. .+..++++.|++|||||||
T Consensus 61 eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~G-~v~~L~~~~~p~t~~lre~Ll~LpGVG~K 126 (177)
T TIGR03252 61 QAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYDG-DATAVWTEGDPDGKELLRRLKALPGFGKQ 126 (177)
T ss_pred HHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhCC-ChhhhhcccCCCcHHHHHHHHcCCCCCHH
Confidence 3 234434 553 3699999999999875332 4555554 4567889999999999999
No 19
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.32 E-value=1.3e-11 Score=125.94 Aligned_cols=123 Identities=24% Similarity=0.440 Sum_probs=99.6
Q ss_pred CCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChH
Q psy4725 125 QDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVE 204 (457)
Q Consensus 125 qDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~E 204 (457)
.+||..++|-|..||+.+.+......++.+ .|||+++||+++.+
T Consensus 32 ~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~------------------------------------rfPti~~LA~A~~~ 75 (342)
T COG1194 32 KDPYRVWVSEIMLQQTQVATVIPYYERFLE------------------------------------RFPTIKALAAAPED 75 (342)
T ss_pred CCcceehhHHHHhhhccHhhhhhhHHHHHH------------------------------------hCCCHHHHhcCCHH
Confidence 479999999999999999887776665544 47999999998765
Q ss_pred HHHHh-cCCch--hHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccchh
Q psy4725 205 AKLRQ-LGFGY--RAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHY 281 (457)
Q Consensus 205 e~LR~-~g~gY--RAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~ 281 (457)
+.|+- -|+|| ||++++.+|+.|.+..|-.+ ++-.+.|.+|||||+.
T Consensus 76 evl~~W~gLGYysRArnL~~~A~~v~~~~~G~~---------P~~~~~l~~LpGiG~y---------------------- 124 (342)
T COG1194 76 EVLKAWEGLGYYSRARNLHKAAQEVVERHGGEF---------PDDEEELAALPGVGPY---------------------- 124 (342)
T ss_pred HHHHHHHhcChHHHHHHHHHHHHHHHHHcCCCC---------CCCHHHHHhCCCCcHH----------------------
Confidence 55553 48885 89999999999999633322 3335778889999999
Q ss_pred hhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhccc
Q psy4725 282 QVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHF 361 (457)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~~ 361 (457)
||..|+.|++++..++ ||+.|.|+..|.|..
T Consensus 125 ------------------------------------------------Ta~Ail~~a~~~~~~~-lDgNV~RVl~R~f~i 155 (342)
T COG1194 125 ------------------------------------------------TAGAILSFAFNQPEPV-LDGNVKRVLSRLFAI 155 (342)
T ss_pred ------------------------------------------------HHHHHHHHHhCCCCce-eecchheeehhhhcc
Confidence 9999999999986444 699999999999875
Q ss_pred CC
Q psy4725 362 QK 363 (457)
Q Consensus 362 ~~ 363 (457)
..
T Consensus 156 ~~ 157 (342)
T COG1194 156 SG 157 (342)
T ss_pred cc
Confidence 43
No 20
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.27 E-value=7.7e-11 Score=113.04 Aligned_cols=141 Identities=20% Similarity=0.276 Sum_probs=109.3
Q ss_pred CHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCCh--
Q psy4725 126 DLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAV-- 203 (457)
Q Consensus 126 DPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~-- 203 (457)
+-.|.++++|+.||+|++.+.+.+++|....- -.+++|...+.
T Consensus 29 ~~~EiiigAILtQNT~WknvekAlenLk~~~~-----------------------------------~~l~~I~~~~~~~ 73 (215)
T COG2231 29 NKDEIIIGAILTQNTSWKNVEKALENLKNEGI-----------------------------------LNLKKILKLDEEE 73 (215)
T ss_pred CchhHHHHHHHhccccHHHHHHHHHHHHHccc-----------------------------------CCHHHHhcCCHHH
Confidence 34599999999999999999999999987521 13667766542
Q ss_pred -HHHHHhcCCc-hhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccchh
Q psy4725 204 -EAKLRQLGFG-YRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHY 281 (457)
Q Consensus 204 -Ee~LR~~g~g-YRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~ 281 (457)
.+.+|..||- .+|++|+++.+.+... ...+.+......|+.|++++|||+-
T Consensus 74 L~elIrpsGFYnqKa~rLk~l~k~l~~~-----~~~~~~~~~~~~R~~LL~iKGIG~E---------------------- 126 (215)
T COG2231 74 LAELIRPSGFYNQKAKRLKALSKNLAKF-----FINLESFKSEVLREELLSIKGIGKE---------------------- 126 (215)
T ss_pred HHHHHhccchHHHHHHHHHHHHHHHHHH-----hhhhhccchHHHHHHHHccCCcchh----------------------
Confidence 2456778883 2599998888877762 2233334444589999999999999
Q ss_pred hhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhccc
Q psy4725 282 QVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHF 361 (457)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~~ 361 (457)
|||.|+|+++.++ +|+||-.-+|++.|.+..
T Consensus 127 ------------------------------------------------TaDsILlYa~~rp-~FVvD~Yt~R~l~rlg~i 157 (215)
T COG2231 127 ------------------------------------------------TADSILLYALDRP-VFVVDKYTRRLLSRLGGI 157 (215)
T ss_pred ------------------------------------------------hHHHHHHHHhcCc-ccchhHHHHHHHHHhccc
Confidence 9999999999995 889999999999998764
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhh
Q psy4725 362 QKSTSKTLTPAVYNQIRAFFADKF 385 (457)
Q Consensus 362 ~~~~~~~lt~~~y~~i~~~~~~~f 385 (457)
.. +.|++|+.+|.+..
T Consensus 158 ~~--------k~ydeik~~fe~~l 173 (215)
T COG2231 158 EE--------KKYDEIKELFEENL 173 (215)
T ss_pred cc--------ccHHHHHHHHHhcc
Confidence 32 25899999887543
No 21
>KOG1921|consensus
Probab=99.25 E-value=8.8e-11 Score=115.16 Aligned_cols=153 Identities=20% Similarity=0.303 Sum_probs=114.0
Q ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCC---h
Q psy4725 127 LTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPA---V 203 (457)
Q Consensus 127 PfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~---~ 203 (457)
-|..|++.++|+|+........+.||.+..|- |++++.+.+ .
T Consensus 78 RfqvLv~lmLSSQTKDevt~~Am~rL~~~~gL-----------------------------------T~e~v~~~de~~l 122 (286)
T KOG1921|consen 78 RFQVLVGLMLSSQTKDEVTAAAMLRLKEYGGL-----------------------------------TLEAVLKIDEPTL 122 (286)
T ss_pred hHHHHHHHHHhcchHHHHHHHHHHHHHHhcCC-----------------------------------CHHHHhccChHhH
Confidence 38999999999999999999999999887542 567777654 2
Q ss_pred HHHHHhcCCchh-HHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcccccccccccCCCccchhh
Q psy4725 204 EAKLRQLGFGYR-AKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQ 282 (457)
Q Consensus 204 Ee~LR~~g~gYR-AkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~ 282 (457)
++.|...||-.| |+||..+|+.+.+..+ -+.+...+.|++|||||||
T Consensus 123 ~~LI~~VgFy~rKA~ylkkta~IL~d~f~---------gDIP~~v~dLlsLPGVGPK----------------------- 170 (286)
T KOG1921|consen 123 NELIYPVGFYTRKAKYLKKTAKILQDKFD---------GDIPDTVEDLLSLPGVGPK----------------------- 170 (286)
T ss_pred HhhhhhccchHHHHHHHHHHHHHHHHHhC---------CCCchhHHHHhcCCCCchH-----------------------
Confidence 344556788655 9999999999988532 2356778999999999999
Q ss_pred hhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhcccC
Q psy4725 283 VYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYHFQ 362 (457)
Q Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~~~ 362 (457)
.|-.++-.+.++..-+-|||||+||..++....
T Consensus 171 -----------------------------------------------Ma~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~ 203 (286)
T KOG1921|consen 171 -----------------------------------------------MAHLTMQVAWNKIVGICVDTHVHRICNRLGWVD 203 (286)
T ss_pred -----------------------------------------------HHHHHHHHHhccceeEEeehHHHHHHHHhcccc
Confidence 888889999999999999999999999988755
Q ss_pred CCCCCCCCH-HHHHHHHHHH-Hhhhc----CcHHHHHHHH
Q psy4725 363 KSTSKTLTP-AVYNQIRAFF-ADKFG----KYAGWAHSIL 396 (457)
Q Consensus 363 ~~~~~~lt~-~~y~~i~~~~-~~~fg----~~ag~A~~~l 396 (457)
. ++-|| ..-.+++..+ .+.|- -.-|+.|.+.
T Consensus 204 ~---ktkspE~TR~aLq~wLPk~lW~eIN~lLVGFGQ~iC 240 (286)
T KOG1921|consen 204 T---KTKSPEQTRVALQQWLPKSLWVEINHLLVGFGQTIC 240 (286)
T ss_pred c---ccCCHHHHHHHHHHhCcHHHHhhhhceeecccceee
Confidence 3 23334 2334444433 23332 2455666554
No 22
>KOG2457|consensus
Probab=98.20 E-value=4.4e-06 Score=86.99 Aligned_cols=117 Identities=21% Similarity=0.453 Sum_probs=90.3
Q ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChHHH
Q psy4725 127 LTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVEAK 206 (457)
Q Consensus 127 PfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~Ee~ 206 (457)
.||.+||-|+-||+.+....+-..+- +-.+||..+|+.++.+++
T Consensus 125 aYeVwVSEiMLQQTrV~TV~~YYt~W------------------------------------MqkwPTl~dla~Asl~~e 168 (555)
T KOG2457|consen 125 AYEVWVSEIMLQQTRVQTVMKYYTRW------------------------------------MQKWPTLYDLAQASLEKE 168 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH------------------------------------HHhCchHHHHHHHHHHHH
Confidence 79999999999999776554433322 234799999999876666
Q ss_pred HHhc--CCch--hHHHHHHHHHHHHHc-CCCCcchhhcCCCHHHHHHHhhc-CCCccccCCCcccccccccccCCCccch
Q psy4725 207 LRQL--GFGY--RAKFIQKSAEYIIQG-GGESWLERLGGKSYEEAREELQR-LPGIGAKVGDGVFKEHVWTLWADPSYLH 280 (457)
Q Consensus 207 LR~~--g~gY--RAkyI~~~A~~~~e~-~G~~~l~~l~~~~~~eare~L~~-LpGVGpK~a~~vl~~~~~~~~~~~~~~~ 280 (457)
..+| |+|| |++.+++.|+.+.+. +|+ .+..-+.|++ +||||++
T Consensus 169 Vn~lWaGlGyY~R~rrL~ega~~vv~~~~ge----------~Prta~~l~kgvpGVG~Y--------------------- 217 (555)
T KOG2457|consen 169 VNELWAGLGYYRRARRLLEGAKMVVAGTEGE----------FPRTASSLMKGVPGVGQY--------------------- 217 (555)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHHhCCCC----------CCChHHHHHhhCCCCCcc---------------------
Confidence 6664 8886 799999999999983 221 2334466776 9999999
Q ss_pred hhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhhcc
Q psy4725 281 YQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNHYH 360 (457)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~y~ 360 (457)
+|-.|+-.+++...-+ ||-.|.|+.+|-..
T Consensus 218 -------------------------------------------------TAGAiaSIAf~q~tGi-VDGNVirvlsRalA 247 (555)
T KOG2457|consen 218 -------------------------------------------------TAGAIASIAFNQVTGI-VDGNVIRVLSRALA 247 (555)
T ss_pred -------------------------------------------------chhhhhhhhhcCcccc-cccchHHHhHHhHh
Confidence 9999999999887655 89999999988653
No 23
>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=97.83 E-value=3.3e-05 Score=68.44 Aligned_cols=76 Identities=16% Similarity=0.214 Sum_probs=52.7
Q ss_pred cCCeEEEEE----CCeEEEEEEcC--CeEEEEEEeCCCCCHHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHhhhhhC
Q psy4725 45 LGNRFQGVF----KECVWTLWADP--SYLHYQVFSQHKLNANSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFV 118 (457)
Q Consensus 45 ~~~~~~gv~----~~~v~~l~q~~--~~L~y~~~~~~~~~~~~~~~~lr~YFdLD~DL~~l~~~~~~~Dp~L~~li~~~~ 118 (457)
.++.|...+ +..+|++...+ +.+.+++..........+..++|++||||.|+..|.+.+ ||.+++++...+
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 356888877 25688888877 577777765555567889999999999999999999998 999999999999
Q ss_pred Ccccc
Q psy4725 119 GIRML 123 (457)
Q Consensus 119 GLRIL 123 (457)
|+|+.
T Consensus 108 GLRlP 112 (116)
T PF06029_consen 108 GLRLP 112 (116)
T ss_dssp T----
T ss_pred CCcCC
Confidence 99984
No 24
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=97.68 E-value=0.00066 Score=65.29 Aligned_cols=159 Identities=22% Similarity=0.314 Sum_probs=110.1
Q ss_pred CCHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCCcHHHHcCCChH
Q psy4725 125 QDLTENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFPSIDALARPAVE 204 (457)
Q Consensus 125 qDPfE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFPTpe~LA~~~~E 204 (457)
.+.|.-|.-.|+.+|.+-...-+|.+.| |+ ..+|. +.++|.
T Consensus 37 e~lf~ELsFCILTANsSA~~~~~~q~~l----G~----------------------------gfly~--~~eEL~----- 77 (210)
T COG1059 37 EDLFKELSFCILTANSSATMGLRAQNEL----GD----------------------------GFLYL--SEEELR----- 77 (210)
T ss_pred HHHHHHHHHHhccccchHHHHHHHHHHh----cc----------------------------ccccC--CHHHHH-----
Confidence 3678888889999999888777777654 32 11222 566654
Q ss_pred HHHHhcCCch---hHHHHHHHHHHHHHcCCCCcchhhcCCC--HHHHHHHhh-cCCCccccCCCcccccccccccCCCcc
Q psy4725 205 AKLRQLGFGY---RAKFIQKSAEYIIQGGGESWLERLGGKS--YEEAREELQ-RLPGIGAKVGDGVFKEHVWTLWADPSY 278 (457)
Q Consensus 205 e~LR~~g~gY---RAkyI~~~A~~~~e~~G~~~l~~l~~~~--~~eare~L~-~LpGVGpK~a~~vl~~~~~~~~~~~~~ 278 (457)
+.|+.+|.-| ||+||+.+=+.+.. +..+-+.+ ..-+|+.|. .++|||-|
T Consensus 78 e~Lk~~g~Rf~n~raeyIVeaR~~~~~------lk~~v~~~~~~~vaRE~Lv~nikGiGyK------------------- 132 (210)
T COG1059 78 EKLKEVGYRFYNVRAEYIVEAREKFDD------LKIIVKADENEKVARELLVENIKGIGYK------------------- 132 (210)
T ss_pred HHHHHhcchhcccchHHHHHHHHHHHH------HHHHHhcCcchHHHHHHHHHHcccccHH-------------------
Confidence 5799888754 79999998877754 23333333 233999999 99999999
Q ss_pred chhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCChHHHHHHHHHhcCCCCccccchhHHHHHHhh
Q psy4725 279 LHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHVYQIACNH 358 (457)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v~~~a~~~ 358 (457)
=|+-. |.-.|.-|.-=+|-||-+-+.+.
T Consensus 133 ---------------------------------------------------EASHF-LRNVG~~D~AIlDrHIlr~l~r~ 160 (210)
T COG1059 133 ---------------------------------------------------EASHF-LRNVGFEDLAILDRHILRWLVRY 160 (210)
T ss_pred ---------------------------------------------------HHHHH-HHhcChhHHHHHHHHHHHHHHHh
Confidence 23222 22334444445799999999988
Q ss_pred cccCCCCCCCCCHHHHHHHHHH---HHhhhcCcHHHHHHHHHhcc
Q psy4725 359 YHFQKSTSKTLTPAVYNQIRAF---FADKFGKYAGWAHSILFCAD 400 (457)
Q Consensus 359 y~~~~~~~~~lt~~~y~~i~~~---~~~~fg~~ag~A~~~lf~~~ 400 (457)
+... +..+++|++.|-.+.+. +++-+|---|---.|+|+..
T Consensus 161 g~i~-e~~kt~t~K~YLe~E~ilr~iae~~g~s~gelDL~IWY~e 204 (210)
T COG1059 161 GLID-ENPKTLTRKLYLEIEEILRSIAEEVGISLGELDLYIWYKE 204 (210)
T ss_pred cccc-cCcccccHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHH
Confidence 7643 33458999998666554 46678888888889999864
No 25
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=95.89 E-value=0.0054 Score=42.43 Aligned_cols=14 Identities=64% Similarity=1.044 Sum_probs=11.6
Q ss_pred HHHHhhcCCCcccc
Q psy4725 246 AREELQRLPGIGAK 259 (457)
Q Consensus 246 are~L~~LpGVGpK 259 (457)
.+++|+++||||||
T Consensus 9 s~eeL~~lpGIG~~ 22 (30)
T PF00633_consen 9 SIEELMKLPGIGPK 22 (30)
T ss_dssp SHHHHHTSTT-SHH
T ss_pred CHHHHHhCCCcCHH
Confidence 36889999999999
No 26
>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=86.51 E-value=0.16 Score=44.21 Aligned_cols=62 Identities=32% Similarity=0.637 Sum_probs=48.2
Q ss_pred CcccccccccccCCCccchhhhhh----ccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhh
Q psy4725 262 DGVFKEHVWTLWADPSYLHYQVYS----QHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFR 323 (457)
Q Consensus 262 ~~vl~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 323 (457)
.+|+.-.+|.+-.++..++|..+. ....+....++.|++||.++.++..+|.+|+++|..+.
T Consensus 32 ~gv~~~~~~~l~q~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~YF~Ld~dl~~l~~~~~~~D~~l~ 97 (117)
T PF07934_consen 32 SGVIGDRVVQLRQDDDNLLYRCLSSAEPSNSSSEEDIEEFLRDYFDLDVDLEKLYEDWSKKDPRLA 97 (117)
T ss_dssp EEEETTEEEEEEEETTEEEEECE--TTS---S-HHHHHHCHHHHTTTTS-HHHHHHHHCCHSHHHH
T ss_pred EEEcCCeEEEEEECCCEEEEEEecCCCcccccchhhHHHHHHHHhcCCccHHHHHHHHhhhCHHHH
Confidence 455666788899888899998887 66667777999999999999999999999999888665
No 27
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.50 E-value=1.8 Score=42.07 Aligned_cols=59 Identities=24% Similarity=0.291 Sum_probs=40.8
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHH------HHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQ------KSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~------~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
...|-|.|.++..- -+.|-. -|.|-| |=.|. +++++|.+ ++ .+.|+++||||+
T Consensus 57 ~~LYGF~t~~Er~l---F~~LisVsGIGPK~ALaILs~~~~~el~~aI~~--~D--------------~~~L~~vpGIGk 117 (196)
T PRK13901 57 LKLFGFLNSSEREV---FEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR--ED--------------IELISKVKGIGN 117 (196)
T ss_pred ceeeCCCCHHHHHH---HHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--CC--------------HHHHhhCCCCCH
Confidence 56899999977542 233333 499988 66666 56666666 32 478999999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|+|.=+
T Consensus 118 KtAeRI 123 (196)
T PRK13901 118 KMAGKI 123 (196)
T ss_pred HHHHHH
Confidence 966444
No 28
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=86.47 E-value=0.57 Score=48.41 Aligned_cols=54 Identities=20% Similarity=0.263 Sum_probs=37.4
Q ss_pred HHHhc-CCchh-HHHHHHHHHHHHHcCCCCc-chhhcCCCHHHHHHHhhcCCCccccCCCcc
Q psy4725 206 KLRQL-GFGYR-AKFIQKSAEYIIQGGGESW-LERLGGKSYEEAREELQRLPGIGAKVGDGV 264 (457)
Q Consensus 206 ~LR~~-g~gYR-AkyI~~~A~~~~e~~G~~~-l~~l~~~~~~eare~L~~LpGVGpK~a~~v 264 (457)
+|..+ |+|-. |+-|.++. .. |... +..+...+.+.+...|+++||||||+|--+
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil---~t--G~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEII---ET--GKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred HHhcCCCccHHHHHHHHHHH---Hh--CcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHH
Confidence 45554 88877 56565543 33 7765 555555667889999999999999955433
No 29
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.85 E-value=0.55 Score=45.04 Aligned_cols=63 Identities=14% Similarity=0.139 Sum_probs=42.1
Q ss_pred HHHHHHHhhcCCCccccCCCcccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhh
Q psy4725 243 YEEAREELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFF 322 (457)
Q Consensus 243 ~~eare~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 322 (457)
..+..+.|+++.|||||+|--+|+ .+..+.+.+|+. .+|- .++.
T Consensus 68 Er~lF~~LisV~GIGpK~Al~iLs---------------------~~~~~~l~~aI~-------------~~D~--~~L~ 111 (186)
T PRK14600 68 EQDCLRMLVKVSGVNYKTAMSILS---------------------KLTPEQLFSAIV-------------NEDK--AALK 111 (186)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHc---------------------cCCHHHHHHHHH-------------cCCH--hheE
Confidence 567889999999999998877776 122333444444 1222 2335
Q ss_pred hccCChHHHHHHHHHhcCC
Q psy4725 323 RQTCGDFVADCICLMSLSH 341 (457)
Q Consensus 323 ~~~~~~~vAdci~l~~l~~ 341 (457)
-|++|.++|.-|++===++
T Consensus 112 vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 112 VNGIGEKLINRIITELQYK 130 (186)
T ss_pred CCCCcHHHHHHHHHHHHHH
Confidence 6999999999998532244
No 30
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.24 E-value=1.1 Score=43.04 Aligned_cols=25 Identities=28% Similarity=0.341 Sum_probs=21.2
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+..+.|+++.|||||+|-.||+
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 3667889999999999998877776
No 31
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=81.95 E-value=0.66 Score=30.59 Aligned_cols=11 Identities=64% Similarity=1.174 Sum_probs=10.1
Q ss_pred HhhcCCCcccc
Q psy4725 249 ELQRLPGIGAK 259 (457)
Q Consensus 249 ~L~~LpGVGpK 259 (457)
.|+++||||+|
T Consensus 2 ~L~~i~GiG~k 12 (26)
T smart00278 2 ELLKVPGIGPK 12 (26)
T ss_pred hhhhCCCCCHH
Confidence 58899999999
No 32
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.32 E-value=1.2 Score=42.81 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=21.2
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+....|+++.|||||+|--||+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 3667889999999999998877776
No 33
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.46 E-value=2.4 Score=40.69 Aligned_cols=59 Identities=22% Similarity=0.304 Sum_probs=38.4
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHH------HHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQ------KSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~------~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
..+|-|.|.++..- -+.|.. -|.|-| |=.|. +++++|.+ |+ .+.|+++||||+
T Consensus 58 ~~LyGF~~~~Er~l---F~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~--~D--------------~~~L~~vpGIGk 118 (188)
T PRK14606 58 ITLYGFSNERKKEL---FLSLTKVSRLGPKTALKIISNEDAETLVTMIAS--QD--------------VEGLSKLPGISK 118 (188)
T ss_pred ceeeCCCCHHHHHH---HHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh--CC--------------HHHHhhCCCCCH
Confidence 56899999877532 223333 488987 54444 34555554 22 478999999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|||.-+
T Consensus 119 KtAerI 124 (188)
T PRK14606 119 KTAERI 124 (188)
T ss_pred HHHHHH
Confidence 966544
No 34
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.35 E-value=2.5 Score=40.61 Aligned_cols=59 Identities=24% Similarity=0.363 Sum_probs=38.2
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHH------HHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQ------KSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~------~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
...|-|.|.++..- -+.|.. -|.|-| |=.|. +++.+|.+ |+ .+.|+++||||+
T Consensus 58 ~~LyGF~~~~Er~l---F~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~--~D--------------~~~L~~vpGIGk 118 (183)
T PRK14601 58 NKLYGFLDKDEQKM---FEMLLKVNGIGANTAMAVCSSLDVNSFYKALSL--GD--------------ESVLKKVPGIGP 118 (183)
T ss_pred ceeeCCCCHHHHHH---HHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh--CC--------------HHHHhhCCCCCH
Confidence 56799999877532 233333 488987 44444 33445544 22 478999999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|+|.=+
T Consensus 119 KtAeRI 124 (183)
T PRK14601 119 KSAKRI 124 (183)
T ss_pred HHHHHH
Confidence 966544
No 35
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.28 E-value=1.1 Score=43.00 Aligned_cols=25 Identities=28% Similarity=0.365 Sum_probs=21.2
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+....|++++|||||+|-.||+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 3677889999999999998877766
No 36
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.68 E-value=1.8 Score=41.80 Aligned_cols=25 Identities=20% Similarity=0.294 Sum_probs=21.0
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+....|+++.|||||+|-.+|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 4677889999999999998877766
No 37
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=77.21 E-value=1.8 Score=41.53 Aligned_cols=25 Identities=24% Similarity=0.420 Sum_probs=20.3
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+....|++++|||||+|-.+|+
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHh
Confidence 3667889999999999997766655
No 38
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.88 E-value=3.4 Score=39.80 Aligned_cols=59 Identities=29% Similarity=0.472 Sum_probs=37.9
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHHHH------HHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQKS------AEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~~~------A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
..+|-|-+.++-.- -+.|-. -|+|-+ |-.|.+. +++|.+ + -.+.|.++||||+
T Consensus 58 ~~LyGF~~~~Er~l---F~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~--~--------------D~~~L~~vpGIGk 118 (194)
T PRK14605 58 LSLFGFATTEELSL---FETLIDVSGIGPKLGLAMLSAMNAEALASAIIS--G--------------NAELLSTIPGIGK 118 (194)
T ss_pred ceeeCCCCHHHHHH---HHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHh--C--------------CHHHHHhCCCCCH
Confidence 56899999876431 223333 388987 6666653 334433 1 1367999999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|+|.-+
T Consensus 119 KtAerI 124 (194)
T PRK14605 119 KTASRI 124 (194)
T ss_pred HHHHHH
Confidence 966443
No 39
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=76.24 E-value=3.2 Score=41.30 Aligned_cols=40 Identities=18% Similarity=0.231 Sum_probs=29.1
Q ss_pred ccccchhHHHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhhc
Q psy4725 344 AVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFG 386 (457)
Q Consensus 344 ~~PvD~~v~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg 386 (457)
++|+||||.|++.+..+.. +|+.+=+.-.+|-+++++.+.
T Consensus 176 iiPLDtHv~~var~LGL~~---rk~~d~k~A~elT~~lr~~~p 215 (232)
T PF09674_consen 176 IIPLDTHVFRVARKLGLLK---RKSADWKAARELTEALREFDP 215 (232)
T ss_pred cccchHhHHHHHHHcCCcc---CCCccHHHHHHHHHHHHhcCC
Confidence 6899999999999987643 345555555677777766553
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.73 E-value=4.1 Score=39.57 Aligned_cols=59 Identities=22% Similarity=0.307 Sum_probs=38.4
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHHH------HHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQK------SAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~~------~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
...|-|.|.++..- -+.|.. -|.|-| |-.|.+ ++++|.+ |+ .+.|+++||||+
T Consensus 59 ~~LyGF~~~~Er~l---F~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~--~D--------------~~~L~~ipGIGk 119 (203)
T PRK14602 59 LELFGFATWDERQT---FIVLISISKVGAKTALAILSQFRPDDLRRLVAE--ED--------------VAALTRVSGIGK 119 (203)
T ss_pred ceeeCCCCHHHHHH---HHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHh--CC--------------HHHHhcCCCcCH
Confidence 56789999877532 233433 488987 544444 3444444 22 478999999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|||.=+
T Consensus 120 KtAerI 125 (203)
T PRK14602 120 KTAQHI 125 (203)
T ss_pred HHHHHH
Confidence 977555
No 41
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.33 E-value=4.3 Score=39.21 Aligned_cols=59 Identities=24% Similarity=0.325 Sum_probs=37.6
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHHH------HHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQK------SAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~~------~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
..+|-|-|.++..- -..|.. -|.|-| |=.|.+ ++.+|.+ ++ .+.|.++||||+
T Consensus 58 ~~LyGF~~~~Er~l---F~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~--~D--------------~~~L~kvpGIGk 118 (195)
T PRK14604 58 LTLYGFSTPAQRQL---FELLIGVSGVGPKAALNLLSSGTPDELQLAIAG--GD--------------VARLARVPGIGK 118 (195)
T ss_pred ceeeCCCCHHHHHH---HHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--CC--------------HHHHhhCCCCCH
Confidence 56788988876431 233433 488987 444433 4445544 22 478999999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|+|.-+
T Consensus 119 KtAerI 124 (195)
T PRK14604 119 KTAERI 124 (195)
T ss_pred HHHHHH
Confidence 977555
No 42
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.09 E-value=2.8 Score=40.52 Aligned_cols=25 Identities=24% Similarity=0.294 Sum_probs=21.0
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+....|+++.|||||+|--||+
T Consensus 66 ~Er~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 66 DSLELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3667889999999999998877766
No 43
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.57 E-value=4.7 Score=39.02 Aligned_cols=59 Identities=24% Similarity=0.411 Sum_probs=37.6
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHHH------HHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQK------SAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~~------~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
...|-|-|.++..- -+.|.. -|.|-| |=.|.+ ++++|.+ |+ .+.|.++||||+
T Consensus 57 ~~LyGF~~~~Er~l---F~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~--~D--------------~~~L~kvpGIGk 117 (197)
T PRK14603 57 LSLYGFPDEDSLEL---FELLLGVSGVGPKLALALLSALPPALLARALLE--GD--------------ARLLTSASGVGK 117 (197)
T ss_pred ceeeCcCCHHHHHH---HHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--CC--------------HHHHhhCCCCCH
Confidence 56788988876431 233433 488887 544433 4455554 22 478999999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|+|.-+
T Consensus 118 KtAerI 123 (197)
T PRK14603 118 KLAERI 123 (197)
T ss_pred HHHHHH
Confidence 977554
No 44
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.43 E-value=4.1 Score=39.15 Aligned_cols=58 Identities=22% Similarity=0.368 Sum_probs=36.7
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHHH------HHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQK------SAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGA 258 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~~------~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGp 258 (457)
..+|-|.|.++..- -+.|.+ -|.|-| |=.|.+ ++++|.+ |+ .+.| ++||||+
T Consensus 58 ~~LyGF~~~~Er~l---F~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~--~D--------------~~~L-~vpGIGk 117 (186)
T PRK14600 58 TQLYGFLNREEQDC---LRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVN--ED--------------KAAL-KVNGIGE 117 (186)
T ss_pred ceeeCCCCHHHHHH---HHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHc--CC--------------Hhhe-ECCCCcH
Confidence 56789999977532 233433 488987 544443 3444444 22 2678 9999999
Q ss_pred cCCCcc
Q psy4725 259 KVGDGV 264 (457)
Q Consensus 259 K~a~~v 264 (457)
|+|.-+
T Consensus 118 KtAerI 123 (186)
T PRK14600 118 KLINRI 123 (186)
T ss_pred HHHHHH
Confidence 977554
No 45
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=72.42 E-value=5.4 Score=38.95 Aligned_cols=57 Identities=25% Similarity=0.356 Sum_probs=33.1
Q ss_pred cccccCCcHHHHcCCChHHHHHhcCCchh-HHHHHH------HHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQLGFGYR-AKFIQK------SAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~~g~gYR-AkyI~~------~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
...|-|.|.++-.- =...++=-|.|=| |=.|.+ ++++|.+ +-.+.|+++||||+|
T Consensus 58 ~~LyGF~~~~ER~l--F~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~----------------~d~~~L~k~PGIGkK 119 (201)
T COG0632 58 HLLYGFLTEEEREL--FRLLISVNGIGPKLALAILSNLDPEELAQAIAN----------------EDVKALSKIPGIGKK 119 (201)
T ss_pred HHHcCCCCHHHHHH--HHHHHccCCccHHHHHHHHcCCCHHHHHHHHHh----------------cChHhhhcCCCCCHH
Confidence 34677887755221 0122233488877 444433 2444443 224789999999999
Q ss_pred CC
Q psy4725 260 VG 261 (457)
Q Consensus 260 ~a 261 (457)
+|
T Consensus 120 tA 121 (201)
T COG0632 120 TA 121 (201)
T ss_pred HH
Confidence 55
No 46
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.21 E-value=3 Score=40.46 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=21.0
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+....|+++.|||||+|--+|+
T Consensus 68 ~Er~lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 68 DERQTFIVLISISKVGAKTALAILS 92 (203)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHh
Confidence 3667889999999999998877766
No 47
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=70.16 E-value=6.5 Score=37.79 Aligned_cols=65 Identities=22% Similarity=0.290 Sum_probs=35.9
Q ss_pred cccccCCcHHHHcCCChHHHHHh-cCCchh-HHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcc
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQ-LGFGYR-AKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGV 264 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~-~g~gYR-AkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~v 264 (457)
..+|-|.|.++..- -..|.. -|+|-| |..|.+.. ..+.|..+=..+-...|.++||||+|+|.=|
T Consensus 57 ~~LyGF~~~~Er~l---F~~L~~V~GIGpK~Al~iL~~~----------~~~el~~aI~~~d~~~L~~ipGiGkKtAerI 123 (191)
T TIGR00084 57 ELLFGFNTLEEREL---FKELIKVNGVGPKLALAILSNM----------SPEEFVYAIETEEVKALVKIPGVGKKTAERL 123 (191)
T ss_pred ceeeCCCCHHHHHH---HHHHhCCCCCCHHHHHHHHhcC----------CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 56899999977542 223333 489976 65553321 1111110001111367999999999965444
No 48
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=68.04 E-value=6.2 Score=39.32 Aligned_cols=39 Identities=23% Similarity=0.297 Sum_probs=27.0
Q ss_pred ccccchhHHHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhh
Q psy4725 344 AVPVDTHVYQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKF 385 (457)
Q Consensus 344 ~~PvD~~v~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~f 385 (457)
++|+||||.|++.++.+.. +|+.+=+.-.+|-+.+++.+
T Consensus 173 iiPLDtH~~rvar~LgL~~---Rk~~d~kaa~ElT~~Lr~~d 211 (229)
T TIGR02757 173 ILPLDTHVFRIAKKLKLLK---RKSYDLKAAIEITEALRELN 211 (229)
T ss_pred eeechHhHHHHHHHhCCcc---cCchhHHHHHHHHHHHHhcC
Confidence 6899999999999886533 34444444566666666554
No 49
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=65.97 E-value=2.5 Score=43.17 Aligned_cols=48 Identities=31% Similarity=0.454 Sum_probs=33.6
Q ss_pred CCchh-HHHHHHHHHHHHHcCCC-CcchhhcCCCHHHHHHHhhcCCCccccCCCcc
Q psy4725 211 GFGYR-AKFIQKSAEYIIQGGGE-SWLERLGGKSYEEAREELQRLPGIGAKVGDGV 264 (457)
Q Consensus 211 g~gYR-AkyI~~~A~~~~e~~G~-~~l~~l~~~~~~eare~L~~LpGVGpK~a~~v 264 (457)
|+|-+ |+-|.++.+ . |+ ..|+.|... ...+...|+++||||||+|.-+
T Consensus 52 giG~~ia~kI~E~~~---t--G~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l 101 (307)
T cd00141 52 GIGKKIAEKIEEILE---T--GKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKL 101 (307)
T ss_pred CccHHHHHHHHHHHH---c--CCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHH
Confidence 88876 666665533 3 44 356666666 7888899999999999955333
No 50
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=65.58 E-value=9.5 Score=30.22 Aligned_cols=34 Identities=41% Similarity=0.583 Sum_probs=20.3
Q ss_pred HHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCC
Q psy4725 222 SAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVG 261 (457)
Q Consensus 222 ~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a 261 (457)
+|+.|.+.-| .++.|...+. +.|++++|||+++|
T Consensus 15 ~ak~L~~~f~--sl~~l~~a~~----e~L~~i~gIG~~~A 48 (64)
T PF12826_consen 15 TAKLLAKHFG--SLEALMNASV----EELSAIPGIGPKIA 48 (64)
T ss_dssp HHHHHHHCCS--CHHHHCC--H----HHHCTSTT--HHHH
T ss_pred HHHHHHHHcC--CHHHHHHcCH----HHHhccCCcCHHHH
Confidence 3455555444 5777877765 57999999999933
No 51
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=62.50 E-value=42 Score=34.14 Aligned_cols=106 Identities=20% Similarity=0.287 Sum_probs=62.7
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHHhCCcccccCCCCCCcCcccCCCCCCCCCCcccccccCC--cHHHHcCCChHH
Q psy4725 128 TENIFSFLCSSNNNIARISGMIDKMCKEYGTLICTLDSDGNLVGDCEKGRSHAKSCPAVTKFFAFP--SIDALARPAVEA 205 (457)
Q Consensus 128 fE~LIsfIcSQNnnI~rI~~mi~rL~~~yGe~l~~~~g~~~~~~~~~~~r~~~~~~p~~~~~ysFP--Tpe~LA~~~~Ee 205 (457)
...|++.|+.- |.-....+|++.|-.++.-+.|| ..++..| .|+++-.+ ...
T Consensus 75 ~~Dfv~Si~dg-----RlfeQ~~rL~~~y~rpvliVegd--------------------~~~~~~~~i~~~av~~a-l~s 128 (254)
T COG1948 75 ISDFVSSIIDG-----RLFEQAKRLKKSYERPVLIVEGD--------------------DSFSRRPKIHPNAVRGA-LAS 128 (254)
T ss_pred HHHHHHHHhcc-----hHHHHHHHHHhcCCccEEEEEcc--------------------cccccccccCHHHHHHH-HHH
Confidence 34566666543 88888999999998887555552 1223323 56666543 222
Q ss_pred HHHhcCCc--h------hHHHHHHHHHHHHHcCCCCc-chhh-cCCCHHHHHHH-hhcCCCcccc
Q psy4725 206 KLRQLGFG--Y------RAKFIQKSAEYIIQGGGESW-LERL-GGKSYEEAREE-LQRLPGIGAK 259 (457)
Q Consensus 206 ~LR~~g~g--Y------RAkyI~~~A~~~~e~~G~~~-l~~l-~~~~~~eare~-L~~LpGVGpK 259 (457)
..-..||. + =|..|+.+|+.....+.... .... ...++++.+.+ |.++||||++
T Consensus 129 ~~vdfg~~vi~t~~~~~Ta~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~ 193 (254)
T COG1948 129 LAVDFGLPVIWTRSPEETAELIHELARREQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPK 193 (254)
T ss_pred HHhhcCceEEEeCCHHHHHHHHHHHHHHHHHhccccccccccccccchHHHHHHHHHcCCCccHH
Confidence 22234554 1 17888888888874222211 1111 23467676654 5699999999
No 52
>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=59.55 E-value=19 Score=27.75 Aligned_cols=15 Identities=40% Similarity=0.773 Sum_probs=13.0
Q ss_pred HHHHHhhcCCCcccc
Q psy4725 245 EAREELQRLPGIGAK 259 (457)
Q Consensus 245 eare~L~~LpGVGpK 259 (457)
.+.+.|+++|||||+
T Consensus 2 ~~~~~L~~I~Gig~~ 16 (60)
T PF14520_consen 2 GVFDDLLSIPGIGPK 16 (60)
T ss_dssp HHHHHHHTSTTCHHH
T ss_pred HHHHhhccCCCCCHH
Confidence 356789999999999
No 53
>PRK08609 hypothetical protein; Provisional
Probab=55.60 E-value=21 Score=39.74 Aligned_cols=47 Identities=38% Similarity=0.548 Sum_probs=31.1
Q ss_pred HHhc-CCchh-HHHHHHHHHHHHHcCCC-CcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 207 LRQL-GFGYR-AKFIQKSAEYIIQGGGE-SWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 207 LR~~-g~gYR-AkyI~~~A~~~~e~~G~-~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
|+++ |+|-+ |+-|.++. .. |. ..|+.|+.. .++....|+++||||||
T Consensus 50 l~~ipgIG~~ia~kI~Eil---~t--G~~~~le~l~~~-~p~~~~~l~~i~GiGpk 99 (570)
T PRK08609 50 FTKLKGIGKGTAEVIQEYR---ET--GESSVLQELKKE-VPEGLLPLLKLPGLGGK 99 (570)
T ss_pred hccCCCcCHHHHHHHHHHH---Hh--CChHHHHHHHhh-CcHHHHHHhcCCCCCHH
Confidence 4443 88887 55555543 23 44 357778764 44555689999999999
No 54
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=53.62 E-value=29 Score=27.58 Aligned_cols=39 Identities=31% Similarity=0.458 Sum_probs=27.6
Q ss_pred CCchhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 211 GFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 211 g~gYRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
|-.||+..-..+|..|.+-. ..+. ...+.|.+|||||++
T Consensus 20 ~~~~r~~aY~~Aa~~i~~l~--~~i~--------~~~~~~~~l~gIG~~ 58 (68)
T PF14716_consen 20 GDPFRARAYRRAAAAIKALP--YPIT--------SGEEDLKKLPGIGKS 58 (68)
T ss_dssp TSHHHHHHHHHHHHHHHHSS--S-HH--------SHHHHHCTSTTTTHH
T ss_pred CCcHHHHHHHHHHHHHHhCC--HhHh--------hHHHHHhhCCCCCHH
Confidence 55689999999999998722 1222 221259999999999
No 55
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=52.77 E-value=9.2 Score=30.77 Aligned_cols=42 Identities=29% Similarity=0.327 Sum_probs=28.8
Q ss_pred HHhcCCchhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 207 LRQLGFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 207 LR~~g~gYRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
+..|||+.||.....- .|-..+..|-..+. +.|+.+||+|++
T Consensus 14 I~~L~LS~Ra~n~L~~-------~~I~tv~dL~~~s~----~~L~~i~n~G~k 55 (66)
T PF03118_consen 14 IEDLGLSVRAYNCLKR-------AGIHTVGDLVKYSE----EDLLKIKNFGKK 55 (66)
T ss_dssp GGGSTSBHHHHHHHHC-------TT--BHHHHHCS-H----HHHHTSTTSHHH
T ss_pred HHHhCCCHHHHHHHHH-------hCCcCHHHHHhCCH----HHHHhCCCCCHh
Confidence 6678999998554332 25556677767765 579999999999
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=49.24 E-value=23 Score=33.92 Aligned_cols=23 Identities=22% Similarity=0.325 Sum_probs=17.1
Q ss_pred HHHHHHHhhcCCCccccCCCccc
Q psy4725 243 YEEAREELQRLPGIGAKVGDGVF 265 (457)
Q Consensus 243 ~~eare~L~~LpGVGpK~a~~vl 265 (457)
..+....|..+||||||+|.-++
T Consensus 68 ek~~f~~L~~i~GIGpk~A~~il 90 (192)
T PRK00116 68 ERELFRLLISVSGVGPKLALAIL 90 (192)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHH
Confidence 34557789999999999554443
No 57
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=48.06 E-value=17 Score=35.69 Aligned_cols=19 Identities=37% Similarity=0.742 Sum_probs=16.5
Q ss_pred HHHHHHHhhcCCCccccCC
Q psy4725 243 YEEAREELQRLPGIGAKVG 261 (457)
Q Consensus 243 ~~eare~L~~LpGVGpK~a 261 (457)
.++.++.|..|||||||+|
T Consensus 7 i~~LI~~l~kLPGvG~KsA 25 (198)
T COG0353 7 IEKLIDALKKLPGVGPKSA 25 (198)
T ss_pred HHHHHHHHhhCCCCChhHH
Confidence 5778899999999999944
No 58
>PRK00076 recR recombination protein RecR; Reviewed
Probab=47.20 E-value=15 Score=35.94 Aligned_cols=17 Identities=53% Similarity=0.874 Sum_probs=15.8
Q ss_pred HHHHHHHhhcCCCcccc
Q psy4725 243 YEEAREELQRLPGIGAK 259 (457)
Q Consensus 243 ~~eare~L~~LpGVGpK 259 (457)
.++..+.|.+|||||+|
T Consensus 6 ~~~Li~~l~~LPGIG~K 22 (196)
T PRK00076 6 IEKLIEALRKLPGIGPK 22 (196)
T ss_pred HHHHHHHHHHCCCCCHH
Confidence 67889999999999999
No 59
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=45.05 E-value=16 Score=36.36 Aligned_cols=56 Identities=30% Similarity=0.343 Sum_probs=40.8
Q ss_pred HHHHcCCChHHHHH-hcCCchhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 195 IDALARPAVEAKLR-QLGFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 195 pe~LA~~~~Ee~LR-~~g~gYRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
++.|++ .|.|- -|+-|-+-+-...+|++|.++-|. |..|..++. ++|+++||||+-
T Consensus 21 ~~~Lsd---~ELLailLrtG~~~~~~~~la~~lL~~fg~--L~~l~~a~~----~el~~v~GiG~a 77 (224)
T COG2003 21 AEALSD---AELLAILLRTGTKGESVLDLAKELLQEFGS--LAELLKASV----EELSSVKGIGLA 77 (224)
T ss_pred hhhcch---HHHHHHHHhcCCCCCCHHHHHHHHHHHccc--HHHHHhCCH----HHHhhCCCccHH
Confidence 566664 23443 256777888889999999996543 667767764 679999999977
No 60
>PRK13844 recombination protein RecR; Provisional
Probab=43.91 E-value=16 Score=35.76 Aligned_cols=20 Identities=35% Similarity=0.544 Sum_probs=17.0
Q ss_pred CHHHHHHHhhcCCCccccCC
Q psy4725 242 SYEEAREELQRLPGIGAKVG 261 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a 261 (457)
..++..+.|.+|||||+|+|
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA 28 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSS 28 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHH
Confidence 36788999999999999933
No 61
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.46 E-value=21 Score=34.93 Aligned_cols=19 Identities=42% Similarity=0.718 Sum_probs=16.6
Q ss_pred HHHHHHHhhcCCCccccCC
Q psy4725 243 YEEAREELQRLPGIGAKVG 261 (457)
Q Consensus 243 ~~eare~L~~LpGVGpK~a 261 (457)
.++..+.|.+|||||+|+|
T Consensus 6 ~~~Li~~l~~LPGIG~KsA 24 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSA 24 (195)
T ss_pred HHHHHHHHHHCCCCCHHHH
Confidence 6788999999999999933
No 62
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=40.31 E-value=2.8 Score=36.63 Aligned_cols=18 Identities=28% Similarity=0.685 Sum_probs=11.9
Q ss_pred HhhcCCCccccCCCcccc
Q psy4725 249 ELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 249 ~L~~LpGVGpK~a~~vl~ 266 (457)
-+-.+||||+|+|--+|.
T Consensus 19 NIPGV~GIG~KtA~~LL~ 36 (101)
T PF01367_consen 19 NIPGVPGIGPKTAAKLLQ 36 (101)
T ss_dssp TB---TTSTCHCCCCCHH
T ss_pred CCCCCCCCCHHHHHHHHH
Confidence 356789999998877655
No 63
>PRK07758 hypothetical protein; Provisional
Probab=39.49 E-value=29 Score=30.38 Aligned_cols=25 Identities=32% Similarity=0.453 Sum_probs=18.9
Q ss_pred CCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 231 GESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 231 G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
|-..+++|...+. ++|++++|+|+|
T Consensus 54 GI~TL~dLv~~te----~ELl~iknlGkK 78 (95)
T PRK07758 54 GIHTVEELSKYSE----KEILKLHGMGPA 78 (95)
T ss_pred CCCcHHHHHcCCH----HHHHHccCCCHH
Confidence 4455666666664 679999999999
No 64
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.27 E-value=10 Score=36.94 Aligned_cols=25 Identities=36% Similarity=0.416 Sum_probs=21.6
Q ss_pred CHHHHHHHhhcCCCccccCCCcccc
Q psy4725 242 SYEEAREELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 242 ~~~eare~L~~LpGVGpK~a~~vl~ 266 (457)
...+..+.|+++.|||||+|--||+
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3677889999999999998888876
No 65
>PTZ00217 flap endonuclease-1; Provisional
Probab=36.05 E-value=8.2 Score=41.07 Aligned_cols=57 Identities=21% Similarity=0.319 Sum_probs=37.5
Q ss_pred HhhcCCCccccCCCcccccccccccCCCccchhhhhhccccccchHHHHHHHHhhhhcCchhhHhhhhchhhhhhccCCh
Q psy4725 249 ELQRLPGIGAKVGDGVFKEHVWTLWADPSYLHYQVYSQHKLNTNSVETMLKEYFRLDENLPELYAEWSNRDAFFRQTCGD 328 (457)
Q Consensus 249 ~L~~LpGVGpK~a~~vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (457)
.+-.+||||||+|--++. .|.+++..|...-+.+-.+|+.|.-..-|..|..|.|-+
T Consensus 236 y~pgi~GIG~ktA~~Li~-----------------------~~gsle~il~~~~~~k~~~p~~~~~~~~~~~f~~p~V~~ 292 (393)
T PTZ00217 236 YCDTIKGIGPKTAYKLIK-----------------------KYKSIEEILEHLDKTKYPVPENFDYKEARELFLNPEVTP 292 (393)
T ss_pred CCCCCCCccHHHHHHHHH-----------------------HcCCHHHHHHHHHhcCCCCCCCCChHHHHHHhcCCCcCC
Confidence 455899999996633333 234566666544433334677777777888888888874
No 66
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=33.85 E-value=24 Score=33.71 Aligned_cols=19 Identities=32% Similarity=0.714 Sum_probs=14.6
Q ss_pred HHHhhcCCCccccCCCccc
Q psy4725 247 REELQRLPGIGAKVGDGVF 265 (457)
Q Consensus 247 re~L~~LpGVGpK~a~~vl 265 (457)
.+.|.++||||+|+|.-|+
T Consensus 107 ~~~L~~v~Gig~k~A~~I~ 125 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIV 125 (192)
T ss_pred HHHHHhCCCCCHHHHHHHH
Confidence 3579999999999665443
No 67
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=33.81 E-value=1.2e+02 Score=24.49 Aligned_cols=49 Identities=27% Similarity=0.348 Sum_probs=32.5
Q ss_pred HHHHhcCCc-hhHHHHHHHHHHHHHcCCCCcchhhc-CCCHHHHHHHhhcC
Q psy4725 205 AKLRQLGFG-YRAKFIQKSAEYIIQGGGESWLERLG-GKSYEEAREELQRL 253 (457)
Q Consensus 205 e~LR~~g~g-YRAkyI~~~A~~~~e~~G~~~l~~l~-~~~~~eare~L~~L 253 (457)
.+|-++||+ +.|+-|+.-|+.+.=..|-.+.+.=+ +.-+..+.++|+.+
T Consensus 7 ~dLi~lGf~~~tA~~IIrqAK~~lV~~G~~~Y~nkRlg~VP~~~VEeiLG~ 57 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQAKALLVQKGFSFYNNKRLGRVPASAVEEILGI 57 (59)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHHcCCCcccCCccCcccHHHHHHHHCC
Confidence 578889998 67988888888776555766665422 22245566666654
No 68
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=33.64 E-value=31 Score=30.01 Aligned_cols=17 Identities=24% Similarity=0.468 Sum_probs=14.5
Q ss_pred HHHHHHHhhcCCCcccc
Q psy4725 243 YEEAREELQRLPGIGAK 259 (457)
Q Consensus 243 ~~eare~L~~LpGVGpK 259 (457)
..+....|+.|||||+.
T Consensus 7 ~~~~~~~L~~iP~IG~a 23 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKA 23 (93)
T ss_pred HHHHHHHHhcCCCccHH
Confidence 34567899999999999
No 69
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.72 E-value=24 Score=34.73 Aligned_cols=44 Identities=25% Similarity=0.240 Sum_probs=34.6
Q ss_pred cCCchhHH-HHHHHHHHHHHcC---CCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 210 LGFGYRAK-FIQKSAEYIIQGG---GESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 210 ~g~gYRAk-yI~~~A~~~~e~~---G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
|+-|.+-+ -...+|+.|.++. | .|..|..++. ++|++++|||+.
T Consensus 24 L~~g~~~~~~~~~lA~~ll~~f~~~g--~l~~l~~a~~----~eL~~i~GiG~a 71 (218)
T TIGR00608 24 LRTGTPKGLDVLSLSKRLLDVFGRQD--SLGHLLSAPP----EELSSVPGIGEA 71 (218)
T ss_pred HhCCCCCCCCHHHHHHHHHHHhcccC--CHHHHHhCCH----HHHHhCcCCcHH
Confidence 57777777 8899999999853 3 4777777775 558899999995
No 70
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=32.36 E-value=23 Score=31.59 Aligned_cols=15 Identities=60% Similarity=0.857 Sum_probs=12.4
Q ss_pred HHHhhcCCCccccCC
Q psy4725 247 REELQRLPGIGAKVG 261 (457)
Q Consensus 247 re~L~~LpGVGpK~a 261 (457)
.+.|+++||||++.|
T Consensus 67 ~~eL~~lpGIG~~~A 81 (120)
T TIGR01259 67 LEELQALPGIGPAKA 81 (120)
T ss_pred HHHHhcCCCCCHHHH
Confidence 467899999999944
No 71
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=32.10 E-value=7.3 Score=30.18 Aligned_cols=19 Identities=16% Similarity=0.321 Sum_probs=12.5
Q ss_pred HHhhcCCCccccCCCcccc
Q psy4725 248 EELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 248 e~L~~LpGVGpK~a~~vl~ 266 (457)
+.++.+.||||.+|.-.+.
T Consensus 2 ~~f~~I~GVG~~tA~~w~~ 20 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYA 20 (52)
T ss_dssp HHHHTSTT--HHHHHHHHH
T ss_pred cchhhcccccHHHHHHHHH
Confidence 5789999999996654443
No 72
>PRK00024 hypothetical protein; Reviewed
Probab=31.90 E-value=27 Score=34.35 Aligned_cols=49 Identities=35% Similarity=0.356 Sum_probs=36.7
Q ss_pred HHHH-hcCCchhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 205 AKLR-QLGFGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 205 e~LR-~~g~gYRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
|.|. -|+.|.+-+-...+|+.|.++.| .|..+..++. ++|++++|||+.
T Consensus 28 ELLa~lL~~g~~~~~~~~LA~~LL~~fg--sL~~l~~as~----~eL~~i~GIG~a 77 (224)
T PRK00024 28 ELLAILLRTGTKGKSVLDLARELLQRFG--SLRGLLDASL----EELQSIKGIGPA 77 (224)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHcC--CHHHHHhCCH----HHHhhccCccHH
Confidence 3443 26788887788899999998544 4667767775 458899999999
No 73
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=31.77 E-value=18 Score=33.63 Aligned_cols=17 Identities=59% Similarity=0.958 Sum_probs=12.7
Q ss_pred HHhhcCCCccccCCCcc
Q psy4725 248 EELQRLPGIGAKVGDGV 264 (457)
Q Consensus 248 e~L~~LpGVGpK~a~~v 264 (457)
++|..+||||+|.|.-|
T Consensus 97 eeL~~lpgIG~~kA~aI 113 (149)
T COG1555 97 EELQALPGIGPKKAQAI 113 (149)
T ss_pred HHHHHCCCCCHHHHHHH
Confidence 45689999999955444
No 74
>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=31.73 E-value=60 Score=25.01 Aligned_cols=32 Identities=25% Similarity=0.460 Sum_probs=24.2
Q ss_pred CCcHHHHcCCChHHHHHhc-CCchh-HHHHHHHHH
Q psy4725 192 FPSIDALARPAVEAKLRQL-GFGYR-AKFIQKSAE 224 (457)
Q Consensus 192 FPTpe~LA~~~~Ee~LR~~-g~gYR-AkyI~~~A~ 224 (457)
|.|+++|+.++ .+.|..+ |+|.+ |..|++.++
T Consensus 26 ~~t~~~l~~a~-~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 26 IKTLEDLANAD-PEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp CSSHHHHHTSH-HHHHHTSTTSSHHHHHHHHHHHH
T ss_pred CCcHHHHHcCC-HHHHhcCCCCCHHHHHHHHHHHh
Confidence 56899999975 4567765 99975 788877665
No 75
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=31.15 E-value=74 Score=36.34 Aligned_cols=32 Identities=25% Similarity=0.301 Sum_probs=18.7
Q ss_pred CcHHHHcCCChHHHHHhc-CCchh-HHHHHHHHHH
Q psy4725 193 PSIDALARPAVEAKLRQL-GFGYR-AKFIQKSAEY 225 (457)
Q Consensus 193 PTpe~LA~~~~Ee~LR~~-g~gYR-AkyI~~~A~~ 225 (457)
-++++|-.+. ++.|..+ |||.+ +..|.+..+.
T Consensus 468 ~~i~DL~~L~-~~~L~~l~gfG~Ksa~~ll~~Ie~ 501 (665)
T PRK07956 468 HDPADLFKLT-AEDLLGLEGFGEKSAQNLLDAIEK 501 (665)
T ss_pred CCHHHHHhcC-HHHHhcCcCcchHHHHHHHHHHHH
Confidence 4566666543 4457666 88875 5565554443
No 76
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=29.66 E-value=1.4e+02 Score=34.05 Aligned_cols=14 Identities=29% Similarity=0.344 Sum_probs=8.9
Q ss_pred ccCChHHHHHHHHH
Q psy4725 324 QTCGDFVADCICLM 337 (457)
Q Consensus 324 ~~~~~~vAdci~l~ 337 (457)
+++|..+|..|.-|
T Consensus 536 ~GIG~~~A~~I~~f 549 (652)
T TIGR00575 536 EGVGPKVAESIVNF 549 (652)
T ss_pred CCcCHHHHHHHHHH
Confidence 35677777776544
No 77
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=26.57 E-value=78 Score=32.89 Aligned_cols=40 Identities=23% Similarity=0.451 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcc
Q psy4725 214 YRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGV 264 (457)
Q Consensus 214 YRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~v 264 (457)
||..+...+|..|.+- ...+.++ +.|.++||||+++|+-|
T Consensus 25 ~k~~ay~~Aa~~i~~l--~~~i~~~---------~~l~~lpgIG~~ia~kI 64 (334)
T smart00483 25 RKCSYFRKAASVLKSL--PFPINSM---------KDLKGLPGIGDKIKKKI 64 (334)
T ss_pred HHHHHHHHHHHHHHhC--CCCCCCH---------HHHhcCCCccHHHHHHH
Confidence 6788888899888762 2233321 36889999999955443
No 78
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=25.55 E-value=1.1e+02 Score=24.07 Aligned_cols=41 Identities=39% Similarity=0.559 Sum_probs=22.6
Q ss_pred HHHHHhc-CCchh-HHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 204 EAKLRQL-GFGYR-AKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 204 Ee~LR~~-g~gYR-AkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
.++|..+ |+|.+ |+.|++-=+. .|+-.. .+.|..++|||++
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~R~~---~G~f~s------------~~dL~~v~gi~~~ 55 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEYREK---NGPFKS------------LEDLKEVPGIGPK 55 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHHHHH---H-S-SS------------GGGGGGSTT--HH
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHh---CcCCCC------------HHHHhhCCCCCHH
Confidence 4568887 99864 7777664332 222211 3568899999988
No 79
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=25.37 E-value=19 Score=29.48 Aligned_cols=19 Identities=32% Similarity=0.662 Sum_probs=13.6
Q ss_pred HHhhcCCCccccCCCcccc
Q psy4725 248 EELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 248 e~L~~LpGVGpK~a~~vl~ 266 (457)
+.+..+||||+|+|.=++.
T Consensus 22 D~i~gv~giG~k~A~~ll~ 40 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLK 40 (75)
T ss_pred ccCCCCCcccHHHHHHHHH
Confidence 4577899999996644433
No 80
>PRK14976 5'-3' exonuclease; Provisional
Probab=24.47 E-value=12 Score=37.92 Aligned_cols=19 Identities=21% Similarity=0.510 Sum_probs=13.7
Q ss_pred HHhhcCCCccccCCCcccc
Q psy4725 248 EELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 248 e~L~~LpGVGpK~a~~vl~ 266 (457)
+-+-.+||||||+|.-+|.
T Consensus 191 DnipGVpGIG~KtA~~LL~ 209 (281)
T PRK14976 191 DNIKGVKGIGPKTAIKLLN 209 (281)
T ss_pred CCCCCCCcccHHHHHHHHH
Confidence 3467789999997755544
No 81
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=23.84 E-value=94 Score=31.87 Aligned_cols=42 Identities=29% Similarity=0.445 Sum_probs=28.8
Q ss_pred CchhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHhhcCCCccccCCCcc
Q psy4725 212 FGYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREELQRLPGIGAKVGDGV 264 (457)
Q Consensus 212 ~gYRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK~a~~v 264 (457)
--||++.-..+|..|.+- ...+.+ .++++++||||+++|+.|
T Consensus 20 ~~~r~~aY~~Aa~~l~~l--~~~i~~---------~~~~~~ipgiG~~ia~kI 61 (307)
T cd00141 20 NPFRVRAYRKAARALESL--PEPIES---------LEEAKKLPGIGKKIAEKI 61 (307)
T ss_pred CcchHHHHHHHHHHHHhC--CcccCC---------HHHhcCCCCccHHHHHHH
Confidence 458988888999888772 222322 235699999999955444
No 82
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.77 E-value=3.1e+02 Score=24.77 Aligned_cols=46 Identities=24% Similarity=0.382 Sum_probs=30.1
Q ss_pred cCCcHHHHcCCChHHHHHhcCC-----chhHHHHHHHHHHHHHcCCCCcchhhcCCCHHHHHHHh
Q psy4725 191 AFPSIDALARPAVEAKLRQLGF-----GYRAKFIQKSAEYIIQGGGESWLERLGGKSYEEAREEL 250 (457)
Q Consensus 191 sFPTpe~LA~~~~Ee~LR~~g~-----gYRAkyI~~~A~~~~e~~G~~~l~~l~~~~~~eare~L 250 (457)
+|||...= .++.++++|+ ........++-++|.+ |+ .+.++|.+.|
T Consensus 62 SYPTvR~r----Ld~ii~~lg~~~~~~~~~~~~~~~IL~~L~~--Ge--------Is~eeA~~~L 112 (113)
T PF09862_consen 62 SYPTVRNR----LDKIIEKLGYEEDEEEEEEDERKEILDKLEK--GE--------ISVEEALEIL 112 (113)
T ss_pred CcHHHHHH----HHHHHHHhCCCCCcccccchhHHHHHHHHHc--CC--------CCHHHHHHHh
Confidence 67887653 3467888888 1234555666666766 65 6788888776
No 83
>PRK07945 hypothetical protein; Provisional
Probab=23.64 E-value=67 Score=33.34 Aligned_cols=43 Identities=28% Similarity=0.472 Sum_probs=28.7
Q ss_pred chhHHHHHHHHHHHHHcCCCCc-chhhcCCCHHHHHH-HhhcCCCccccCCCcc
Q psy4725 213 GYRAKFIQKSAEYIIQGGGESW-LERLGGKSYEEARE-ELQRLPGIGAKVGDGV 264 (457)
Q Consensus 213 gYRAkyI~~~A~~~~e~~G~~~-l~~l~~~~~~eare-~L~~LpGVGpK~a~~v 264 (457)
-||.+.-.++|+.|..- ... +..+. .+ .|+++||||.-+|..|
T Consensus 21 ~frv~ayr~aa~~~~~~--~~~~~~~~~-------~~g~l~~~~giG~~~a~~i 65 (335)
T PRK07945 21 TYRVRAFRRAADVVEAL--DAAERARRA-------RAGSLTSLPGIGPKTAKVI 65 (335)
T ss_pred hhhHHHHHHHHHHHHhc--ChhHHHHHH-------hcCCcccCCCcCHHHHHHH
Confidence 38999999999988762 111 22211 12 6999999999955444
No 84
>KOG2841|consensus
Probab=22.76 E-value=81 Score=32.04 Aligned_cols=38 Identities=26% Similarity=0.372 Sum_probs=30.2
Q ss_pred cccccCCcHHHHcCCChHHHHHhc-CCch-hHHHHHHHHHH
Q psy4725 187 TKFFAFPSIDALARPAVEAKLRQL-GFGY-RAKFIQKSAEY 225 (457)
Q Consensus 187 ~~~ysFPTpe~LA~~~~Ee~LR~~-g~gY-RAkyI~~~A~~ 225 (457)
.....|+|.++|..++ +++|.+| |+|- +|+.|++.-..
T Consensus 210 ~LL~~FgsLq~~~~AS-~~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 210 LLLQKFGSLQQISNAS-EGELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHhcccHHHHHhcC-HhHHHhCcCcCHHHHHHHHHHHhc
Confidence 3467899999999986 6678886 9996 49999887543
No 85
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=21.66 E-value=1.6e+02 Score=27.56 Aligned_cols=37 Identities=19% Similarity=0.416 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHh-ccccHHHHHHHHHHHHHHhCCcc
Q psy4725 124 NQDLTENIFSFLCS-SNNNIARISGMIDKMCKEYGTLI 160 (457)
Q Consensus 124 rqDPfE~LIsfIcS-QNnnI~rI~~mi~rL~~~yGe~l 160 (457)
.+|+||-++.+|.+ .+.+-..+..+++++.+.||..+
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 47999999999999 88899999999999999999654
No 86
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=21.14 E-value=2.1e+02 Score=30.46 Aligned_cols=39 Identities=23% Similarity=0.381 Sum_probs=31.6
Q ss_pred cccCCcHHHHcCCChHHHHHhc-CCc-hhHHHHHHHHHHHHH
Q psy4725 189 FFAFPSIDALARPAVEAKLRQL-GFG-YRAKFIQKSAEYIIQ 228 (457)
Q Consensus 189 ~ysFPTpe~LA~~~~Ee~LR~~-g~g-YRAkyI~~~A~~~~e 228 (457)
.-.|-+...|.+++ .++|.+. |+| .||+.|.+.++.+.+
T Consensus 304 l~~FGSL~~Il~As-~eeL~~VeGIGe~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 304 VEHFGSLQGLLAAS-IEDLDEVEGIGEVRARAIREGLSRLAE 344 (352)
T ss_pred HHHcCCHHHHHcCC-HHHHhhCCCcCHHHHHHHHHHHHHHHH
Confidence 34688999999886 4578875 899 589999999988876
No 87
>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=20.65 E-value=1.2e+02 Score=24.14 Aligned_cols=37 Identities=27% Similarity=0.393 Sum_probs=29.1
Q ss_pred cCCc-HHHHcCCChHHHHHhcCCchhH-HHHHHHHHHHHH
Q psy4725 191 AFPS-IDALARPAVEAKLRQLGFGYRA-KFIQKSAEYIIQ 228 (457)
Q Consensus 191 sFPT-pe~LA~~~~Ee~LR~~g~gYRA-kyI~~~A~~~~e 228 (457)
.||+ .++|-..+. ..|+.+|+--|. +||....+....
T Consensus 18 kf~~~w~~lf~~~s-~~LK~~GIp~r~RryiL~~~ek~r~ 56 (57)
T PF09597_consen 18 KFESDWEKLFTTSS-KQLKELGIPVRQRRYILRWREKYRQ 56 (57)
T ss_pred HHHHHHHHHHhcCH-HHHHHCCCCHHHHHHHHHHHHHHhC
Confidence 4778 889988765 579999998775 999988776543
No 88
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=20.52 E-value=38 Score=23.54 Aligned_cols=10 Identities=40% Similarity=0.800 Sum_probs=7.8
Q ss_pred hhcCCCcccc
Q psy4725 250 LQRLPGIGAK 259 (457)
Q Consensus 250 L~~LpGVGpK 259 (457)
+..++|||++
T Consensus 13 i~~~~GIG~k 22 (32)
T PF11798_consen 13 IRKFWGIGKK 22 (32)
T ss_dssp GGGSTTS-HH
T ss_pred HHhhCCccHH
Confidence 5689999999
No 89
>PRK09482 flap endonuclease-like protein; Provisional
Probab=20.40 E-value=31 Score=34.88 Aligned_cols=19 Identities=21% Similarity=0.506 Sum_probs=13.7
Q ss_pred HHhhcCCCccccCCCcccc
Q psy4725 248 EELQRLPGIGAKVGDGVFK 266 (457)
Q Consensus 248 e~L~~LpGVGpK~a~~vl~ 266 (457)
+-+-.+||||||+|--+|.
T Consensus 182 DnIpGVpGIG~KtA~~LL~ 200 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLN 200 (256)
T ss_pred cCCCCCCCcChHHHHHHHH
Confidence 3466789999997755544
No 90
>COG4324 Predicted aminopeptidase [General function prediction only]
Probab=20.07 E-value=1.3e+02 Score=31.33 Aligned_cols=98 Identities=19% Similarity=0.187 Sum_probs=59.9
Q ss_pred hhhhhhccccccch-----HHHHHHHHhhhhcCchhhHhh---hhchhhhhhccCChHHHHHHHHHhcCCCCccccchhH
Q psy4725 280 HYQVYSQHKLNTNS-----VETMLKEYFRLDENLPELYAE---WSNRDAFFRQTCGDFVADCICLMSLSHLQAVPVDTHV 351 (457)
Q Consensus 280 ~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~vAdci~l~~l~~~~~~PvD~~v 351 (457)
|-.+|...|--||. |+|.=-++-....-+|+-+.+ -++|++-|.-++-..-+..-.|++ -|++..-
T Consensus 207 HQk~Y~~~DtAFNEsFAtaVEt~Gvr~Wl~~~g~p~~~~ry~t~~kRr~qF~aLil~~R~rLealYa------sP~~d~~ 280 (376)
T COG4324 207 HQKIYVNNDTAFNESFATAVETSGVRKWLRATGDPAGLRRYETNRKRRAQFLALILETRDRLEALYA------SPRADEQ 280 (376)
T ss_pred hheEeecCcchHhHHHHHHHHHHhHHHHHHhcCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhc------CCCChHH
Confidence 55566677777764 566666666777789988777 889999888777665555555554 3676654
Q ss_pred HHHHHhhcccCCCCCCCCCHHHHHHHHHHHHhhhcCcHHHHH
Q psy4725 352 YQIACNHYHFQKSTSKTLTPAVYNQIRAFFADKFGKYAGWAH 393 (457)
Q Consensus 352 ~~~a~~~y~~~~~~~~~lt~~~y~~i~~~~~~~fg~~ag~A~ 393 (457)
.+..+.--+.. | ...|.+++ ..+||.|+||-.
T Consensus 281 kragKaA~fdr------L-R~~Ya~l~---~r~WgGy~gyda 312 (376)
T COG4324 281 KRAGKAATFDR------L-RMRYAQLR---DRRWGGYRGYDA 312 (376)
T ss_pred HhhhhHHHHHH------H-HHHHHHhh---hcccCCccchhH
Confidence 44444321110 0 12244433 356888888754
No 91
>PRK14973 DNA topoisomerase I; Provisional
Probab=20.05 E-value=2e+02 Score=34.45 Aligned_cols=65 Identities=17% Similarity=0.207 Sum_probs=39.5
Q ss_pred cCCcHHHHcCCChHHHHHhcCCch-hHHHHHHHHH-HHHHcCCCCcchhhcCCCHHHHHHHhhcCCCcccc
Q psy4725 191 AFPSIDALARPAVEAKLRQLGFGY-RAKFIQKSAE-YIIQGGGESWLERLGGKSYEEAREELQRLPGIGAK 259 (457)
Q Consensus 191 sFPTpe~LA~~~~Ee~LR~~g~gY-RAkyI~~~A~-~~~e~~G~~~l~~l~~~~~~eare~L~~LpGVGpK 259 (457)
-|-+|++++.+++++..-..|++- .+.-....|. .+.. ..-........++.+.+|+.++|||++
T Consensus 822 G~~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~el~~vkg~ge~ 888 (936)
T PRK14973 822 GFDTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGR----PVPEKISKAAFERGRAELLSVPGLGET 888 (936)
T ss_pred cCCCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcC----CCchhhhhhhhcccchhhhhccCCCHH
Confidence 488999999987654334468863 4444433333 3322 222222234445555669999999999
Done!