Query psy12450
Match_columns 168
No_of_seqs 156 out of 1276
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 19:37:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0969|consensus 100.0 1.4E-36 3.1E-41 276.5 8.7 135 31-167 507-650 (1066)
2 PTZ00166 DNA polymerase delta 100.0 2.9E-35 6.3E-40 281.8 11.2 125 41-167 517-643 (1054)
3 PHA02524 43A DNA polymerase su 100.0 4E-34 8.6E-39 255.0 9.2 153 2-158 306-478 (498)
4 cd05534 POLBc_zeta DNA polymer 100.0 1.7E-33 3.7E-38 249.7 10.7 127 41-167 12-162 (451)
5 cd05533 POLBc_delta DNA polyme 100.0 7.5E-33 1.6E-37 242.0 10.1 106 60-167 1-106 (393)
6 KOG0970|consensus 100.0 8.4E-33 1.8E-37 258.6 9.2 155 1-167 732-920 (1429)
7 PHA02528 43 DNA polymerase; Pr 100.0 2.1E-32 4.5E-37 257.9 9.8 115 41-159 357-479 (881)
8 TIGR00592 pol2 DNA polymerase 100.0 5.2E-31 1.1E-35 255.0 8.4 153 2-167 704-888 (1172)
9 PHA03036 DNA polymerase; Provi 100.0 5.5E-30 1.2E-34 241.8 10.0 125 42-167 511-655 (1004)
10 cd05532 POLBc_alpha DNA polyme 100.0 1.6E-29 3.5E-34 221.4 9.0 101 57-167 3-103 (400)
11 cd05536 POLBc_B3 DNA polymeras 100.0 2.5E-29 5.5E-34 218.3 9.0 97 60-166 2-99 (371)
12 PRK05761 DNA polymerase I; Rev 100.0 3.4E-29 7.5E-34 234.5 10.4 156 2-167 319-506 (787)
13 PRK05762 DNA polymerase II; Re 100.0 1.9E-29 4.2E-34 236.4 8.5 146 2-157 330-487 (786)
14 PF00136 DNA_pol_B: DNA polyme 100.0 7.3E-30 1.6E-34 226.5 0.6 126 41-166 12-153 (466)
15 cd00145 POLBc DNA polymerase t 100.0 2.1E-28 4.5E-33 209.0 8.9 99 60-167 1-100 (323)
16 COG0417 PolB DNA polymerase el 100.0 1.9E-28 4.1E-33 229.8 9.3 116 41-167 385-501 (792)
17 cd05530 POLBc_B1 DNA polymeras 99.9 4.5E-28 9.8E-33 210.6 9.5 99 59-167 10-111 (372)
18 cd05531 POLBc_B2 DNA polymeras 99.9 7.7E-27 1.7E-31 201.6 9.1 91 60-161 3-93 (352)
19 PHA03334 putative DNA polymera 99.9 5.1E-27 1.1E-31 224.0 8.6 109 59-167 630-758 (1545)
20 cd05537 POLBc_Pol_II DNA polym 99.9 1.8E-26 4E-31 200.5 8.9 89 61-157 2-90 (371)
21 smart00486 POLBc DNA polymeras 99.9 2.1E-25 4.7E-30 194.2 11.0 122 41-162 255-390 (471)
22 KOG0968|consensus 99.9 1.3E-25 2.7E-30 210.8 3.4 126 41-166 923-1070(1488)
23 cd05538 POLBc_Pol_II_B DNA pol 99.9 2E-24 4.4E-29 186.3 7.4 76 61-167 2-77 (347)
24 TIGR00592 pol2 DNA polymerase 99.2 2.8E-12 6.1E-17 125.2 0.2 131 30-165 452-604 (1172)
25 KOG0969|consensus 98.2 4.7E-07 1E-11 84.6 2.0 34 8-41 789-822 (1066)
26 PHA02563 DNA polymerase; Provi 97.6 3.4E-05 7.3E-10 71.7 2.3 42 59-101 235-279 (630)
27 KOG0968|consensus 97.2 0.00016 3.6E-09 70.2 2.3 32 8-39 1206-1237(1488)
28 PTZ00166 DNA polymerase delta 96.0 0.0024 5.1E-08 62.8 0.8 32 8-39 783-814 (1054)
29 PF03175 DNA_pol_B_2: DNA poly 95.6 0.0039 8.4E-08 55.6 0.5 35 58-93 202-236 (459)
30 cd00145 POLBc DNA polymerase t 93.4 0.046 9.9E-07 46.9 2.0 29 8-36 229-257 (323)
31 cd05537 POLBc_Pol_II DNA polym 93.4 0.04 8.8E-07 48.3 1.6 32 8-39 236-267 (371)
32 cd05533 POLBc_delta DNA polyme 93.4 0.05 1.1E-06 48.0 2.2 32 8-39 245-276 (393)
33 cd05534 POLBc_zeta DNA polymer 93.4 0.047 1E-06 49.1 2.0 32 8-39 297-328 (451)
34 cd05531 POLBc_B2 DNA polymeras 93.3 0.042 9.2E-07 47.9 1.6 32 8-39 215-246 (352)
35 cd05535 POLBc_epsilon DNA poly 93.0 0.046 1E-06 50.9 1.5 29 79-107 92-120 (621)
36 cd05536 POLBc_B3 DNA polymeras 92.7 0.065 1.4E-06 46.9 1.9 32 8-39 221-252 (371)
37 cd05532 POLBc_alpha DNA polyme 92.5 0.052 1.1E-06 48.0 1.0 32 8-39 233-264 (400)
38 cd05538 POLBc_Pol_II_B DNA pol 91.6 0.12 2.6E-06 45.0 2.3 28 8-35 200-227 (347)
39 PHA03036 DNA polymerase; Provi 91.4 0.11 2.3E-06 51.1 1.9 31 8-38 827-860 (1004)
40 PHA02528 43 DNA polymerase; Pr 91.4 0.11 2.5E-06 50.4 2.1 30 9-38 706-735 (881)
41 COG0417 PolB DNA polymerase el 91.3 0.085 1.8E-06 50.6 1.1 35 8-42 628-662 (792)
42 PF00136 DNA_pol_B: DNA polyme 91.1 0.19 4.1E-06 45.0 3.0 33 8-40 288-320 (466)
43 cd05530 POLBc_B1 DNA polymeras 90.9 0.13 2.9E-06 45.2 1.8 32 8-39 229-260 (372)
44 PHA02735 putative DNA polymera 90.6 0.15 3.2E-06 46.1 1.8 42 59-102 269-310 (716)
45 PRK05761 DNA polymerase I; Rev 90.3 0.15 3.1E-06 49.1 1.7 33 8-40 624-656 (787)
46 PRK05762 DNA polymerase II; Re 87.5 0.29 6.2E-06 47.0 1.5 32 8-39 634-665 (786)
47 KOG1798|consensus 77.5 0.82 1.8E-05 46.8 0.3 28 79-106 598-625 (2173)
48 cd05535 POLBc_epsilon DNA poly 71.3 1.6 3.6E-05 40.8 0.6 33 8-40 436-468 (621)
49 KOG0970|consensus 52.7 11 0.00024 38.0 2.5 31 9-39 1051-1081(1429)
50 PF08988 DUF1895: Protein of u 50.0 25 0.00053 23.6 3.2 31 137-167 16-46 (68)
51 TIGR02501 type_III_yscE type I 47.9 28 0.0006 23.3 3.2 30 137-166 15-44 (67)
52 PF07920 DUF1684: Protein of u 34.7 66 0.0014 24.6 3.9 44 44-88 68-112 (143)
53 PRK15366 type III secretion sy 33.9 70 0.0015 22.2 3.5 29 138-166 19-47 (80)
54 COG0163 UbiX 3-polyprenyl-4-hy 30.8 23 0.00049 28.6 0.8 65 14-79 79-159 (191)
55 KOG4498|consensus 24.3 79 0.0017 25.6 2.8 60 12-76 56-121 (197)
56 PF15005 IZUMO: Izumo sperm-eg 23.1 56 0.0012 25.6 1.7 29 140-168 91-119 (160)
57 PF13854 Kelch_5: Kelch motif 22.4 67 0.0014 18.6 1.6 21 64-86 21-41 (42)
58 PF13322 DUF4092: Domain of un 22.1 26 0.00057 27.6 -0.3 14 84-101 152-165 (172)
59 KOG3039|consensus 21.0 1.1E+02 0.0023 26.0 3.1 32 118-157 56-87 (303)
No 1
>KOG0969|consensus
Probab=100.00 E-value=1.4e-36 Score=276.54 Aligned_cols=135 Identities=57% Similarity=0.991 Sum_probs=121.9
Q ss_pred HHHHhccCCC--------ccccccceeeeeCCCCCC-CcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccc
Q psy12450 31 QKLLINRDPD--------GAVTQKNFIIPTYHGGQG-EDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTT 101 (168)
Q Consensus 31 ~~lli~r~~~--------~A~~~~~~liP~~~~~~~-~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~T 101 (168)
..+|..|.+. -++.++++++|+...... .++||||+|+||+.|+|+.||++|||||||||||||||+||+|
T Consensus 507 ~syLltRGqqIKVlSqLlRkakq~~~~~P~i~~~~s~~e~yEGatVIEp~kGfY~~PIATLDFaSLYPSIMmahNLCYtT 586 (1066)
T KOG0969|consen 507 ISYLLTRGQQIKVLSQLLRKAKQKDFVIPNIKSQGSDDEQYEGATVIEPRKGFYDKPIATLDFASLYPSIMMAHNLCYTT 586 (1066)
T ss_pred HHHHHhCCcchHHHHHHHHHHhhcCeeeeeecccCCccccccccEEeecccccCCCCceeeehhhhhhHHHHHhhhhhee
Confidence 3667777752 578889999999964433 3789999999999999999999999999999999999999999
Q ss_pred cccccccccCCCCCCceeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 102 LLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 102 l~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
++.++...+++ +++++.+|+|..|++.+.++|+||++|++||+.||.+|+.||+++||++|++|
T Consensus 587 Ll~~~t~~~l~--~~~~~~TP~g~yFv~~~~rkGlLP~ILe~ll~aRKraK~dlk~ekDp~kr~vl 650 (1066)
T KOG0969|consen 587 LLTKETVEKLG--DEDYTRTPTGDYFVKTEVRKGLLPEILEDLLTARKRAKADLKKEKDPFKRAVL 650 (1066)
T ss_pred ccccchhhhcC--ccceeECCCCCeeeehhhhccccHHHHHHHHHHHHHHHHHHHhccCHHHHhhh
Confidence 99988766554 78999999999999999999999999999999999999999999999999987
No 2
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=2.9e-35 Score=281.81 Aligned_cols=125 Identities=50% Similarity=0.905 Sum_probs=111.7
Q ss_pred ccccccceeeeeCCCC--CCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCce
Q psy12450 41 GAVTQKNFIIPTYHGG--QGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQY 118 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~--~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~ 118 (168)
+.++++|+++|+.... ....+|+||+|+||++|+|++||++|||+|||||||++|||||||++++.+.. .++.+++
T Consensus 517 r~~~~~~~viP~~~~~~~~~~~~yeGg~VleP~~G~y~~pV~vLDF~SLYPSIiia~NlcysTl~~~~~~~--~~~~~~~ 594 (1054)
T PTZ00166 517 RKCKKLNYVIPTVKYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDAN--NYPEDTY 594 (1054)
T ss_pred HHHHhcCeeccCchhccccccCCCCCceeecCCCCCeeCceEEeecCCcccHHHHhcCCCcceeecchhhc--cCCCcce
Confidence 6788999999998532 34578999999999999999999999999999999999999999999876432 2345678
Q ss_pred eeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 119 SKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 119 ~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
..+|+|.+|+++++++||+|++|++|++.|+++|++||+++||+++++|
T Consensus 595 ~~~p~g~~Fv~~~~r~Gilp~iL~~Ll~~R~~~K~~mk~~~d~~~~~~l 643 (1054)
T PTZ00166 595 VTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLLKKVL 643 (1054)
T ss_pred eecCCCceeeecCCCCcccHHHHHHHHHHHHHHHHHHhhCCCHHHHHHH
Confidence 8899999999988899999999999999999999999999999998875
No 3
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=100.00 E-value=4e-34 Score=254.98 Aligned_cols=153 Identities=24% Similarity=0.299 Sum_probs=114.2
Q ss_pred ccccchhhhhhhhhccC-cHHHHHHHHHH------HHHHHhccCC-----CccccccceeeeeCCCCCCCcccCccEeec
Q psy12450 2 LRHVTWRDGLETVRRDN-SPLVANMINTC------LQKLLINRDP-----DGAVTQKNFIIPTYHGGQGEDQFEGATVIE 69 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~~-c~Lv~~i~~~~------L~~lli~r~~-----~~A~~~~~~liP~~~~~~~~~~y~Gg~Vle 69 (168)
|++|..+|+..+++++. .-|...++..+ +..+..+... ...++++|+++|+.. ....++|+||+|++
T Consensus 306 la~YclkDa~L~~~L~~~~~ll~~~~~larvtglpl~~v~~qikv~~~lllr~~~~~g~viP~~~-~~~~~~Y~GA~V~e 384 (498)
T PHA02524 306 YVDYCVRDTDIILLIDGRRCFIDLILSLSYYAKIRFDDVLGTIKVWDSIIFNSLVESNVVIPAMK-ASPKQSFPGAYVKE 384 (498)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHhccHHHHHHHHHHHHHHHCCEecCCCC-CCCCCccCCeEEec
Confidence 45677777777766653 22222222211 3233211111 157888999999984 44457899999999
Q ss_pred ccCccccCCeEEeecCCcChhHHHhhcCCccccccccccc---c-----CCCCCCceeeCCCceEEeecCCCCcchHHHH
Q psy12450 70 PKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTIT---K-----LELTPDQYSKTPCGNFFLKSSLRKGLLPEIL 141 (168)
Q Consensus 70 P~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~---~-----~~~~~~~~~~~p~~~~f~~~~~~~Gilp~~L 141 (168)
|.||+|++ |++|||+|||||||++|||||+|+++....+ . ...+.++++.+|+|++|++ .++||+|++|
T Consensus 385 P~~GlY~~-VivLDFaSLYPSII~a~NIsPeTl~~~~~~~~~~~~~~~~~~~~~~~~~~~P~G~~F~K--~~~GilP~iL 461 (498)
T PHA02524 385 PVPGGYRY-GLSFDLTSLYPSILRLLNISPEMIAGMFSPARLEDYINKVAPKPSDQFSCAPNGMMYKK--GVVGVLPNET 461 (498)
T ss_pred CCCccccC-eEEEEccccCHHHHHHhCCCHHHhhccccccchhhhccccCCCCCcceEECCCCCEEec--CCCcccHHHH
Confidence 99999999 6789999999999999999999998653211 1 1224678999999999988 4799999999
Q ss_pred HHHHHHHHHHHHHhccC
Q psy12450 142 ENLLSARKQAKNDLKKE 158 (168)
Q Consensus 142 ~~ll~~R~~~K~~mk~~ 158 (168)
++|+++|+++|++|+++
T Consensus 462 e~Ll~~RK~~Kk~M~~a 478 (498)
T PHA02524 462 EKVFLQRKSEKKMMLAA 478 (498)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 99999999999999984
No 4
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Probab=100.00 E-value=1.7e-33 Score=249.72 Aligned_cols=127 Identities=39% Similarity=0.623 Sum_probs=104.2
Q ss_pred ccccccceeeeeCCCCC---CCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccccccccccc-------
Q psy12450 41 GAVTQKNFIIPTYHGGQ---GEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITK------- 110 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~~---~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~------- 110 (168)
+.+++.||++|+..... ....++||+|+||++|+|++||++|||+|||||||++|||||||+++..+...
T Consensus 12 r~~~~~g~~~p~~~~~~~~~~~~~~~g~~V~eP~~G~y~~~V~vLDF~SLYPSIi~~~Nic~sT~~~~~~~~~~~~~~~~ 91 (451)
T cd05534 12 RLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRVEELNGGGKFGF 91 (451)
T ss_pred HHHHHcCEEeecCchhccccccccccCcEeecCCcCcccCceEEEecccccHHHHHHhCcCccccccccccccccccccc
Confidence 45789999999984222 23457899999999999999999999999999999999999999987532110
Q ss_pred -------------CCCCCCceeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCC-hhhhhcc
Q psy12450 111 -------------LELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETD-ELTQVLY 167 (168)
Q Consensus 111 -------------~~~~~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~D-p~~k~~l 167 (168)
.....+++..+|++.+|++++.++||+|++|++|++.|+++|++||+++| +.++++|
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~iL~~Ll~~R~~~K~~mk~~~~~~~~~~~l 162 (451)
T cd05534 92 LGVKLYLPPPPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRIL 162 (451)
T ss_pred ccccccccccccccccCCCcEEECCCcceeecCCCCCCchHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHH
Confidence 01113457778999999998889999999999999999999999999886 7776654
No 5
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=99.98 E-value=7.5e-33 Score=241.97 Aligned_cols=106 Identities=69% Similarity=1.110 Sum_probs=95.5
Q ss_pred cccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcchHH
Q psy12450 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPE 139 (168)
Q Consensus 60 ~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~ 139 (168)
++|+||+|++|++|+|++||++|||+|||||||++|||||||+++..+.. .++.+++..+|++.+|+++++++||+|+
T Consensus 1 ~~Y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~T~~~~~~~~--~~~~~~~~~~p~~~~f~~~~~~~Gilp~ 78 (393)
T cd05533 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAK--KLPPEDYIKTPNGDYFVKSSVRKGLLPE 78 (393)
T ss_pred CCCCCeEeccCCCCCccCCeEEecCCCccHHHHHHhCcCccccccCcccc--cCCCcceEECCCCceeecCCCCCCchHH
Confidence 46999999999999999999999999999999999999999999876543 2335677889999999987789999999
Q ss_pred HHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 140 ILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 140 ~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
+|++|++.|+++|++|++++||.++++|
T Consensus 79 iL~~Ll~~R~~~K~~mk~~~d~~~~~~l 106 (393)
T cd05533 79 ILEELLAARKRAKKDLKEETDPFKKAVL 106 (393)
T ss_pred HHHHHHHHHHHHHHHHhhCCCHHHHHHH
Confidence 9999999999999999999999987654
No 6
>KOG0970|consensus
Probab=99.98 E-value=8.4e-33 Score=258.60 Aligned_cols=155 Identities=32% Similarity=0.496 Sum_probs=131.6
Q ss_pred Cccccchhhhhhhhhc---cC-cHHHHHHHHHH---H-HHHHhccCCC------ccccccceeeeeCCC-----------
Q psy12450 1 MLRHVTWRDGLETVRR---DN-SPLVANMINTC---L-QKLLINRDPD------GAVTQKNFIIPTYHG----------- 55 (168)
Q Consensus 1 ~~~~~~~~~~~~~~r~---~~-c~Lv~~i~~~~---L-~~lli~r~~~------~A~~~~~~liP~~~~----------- 55 (168)
+|++++|+|..++.|+ .| .||.-||.|++ | ++|++.|+++ |+++++||++|.+..
T Consensus 732 ~ll~~~~~d~~~~l~i~~~l~~LpLs~qlTnIaGni~~RTL~G~RAeRnEylLLH~F~~~~fIvPDK~~ssk~~~d~d~~ 811 (1429)
T KOG0970|consen 732 YLLEHTITDAELILQIMFRLNALPLSKQLTNIAGNIWARTLQGGRAERNEYLLLHEFYKNGFIVPDKQNSSKAQKDADET 811 (1429)
T ss_pred HHHHHHhHHHHHHHHHHHHhccchHHHHHHHHHhHHHHHHhhccchhhhhHHHHHHHHHCCccCCCccchhhhhhhhhhh
Confidence 4789999999999998 55 99999999999 5 7888999985 999999999998851
Q ss_pred -C--------CCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceE
Q psy12450 56 -G--------QGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNF 126 (168)
Q Consensus 56 -~--------~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~ 126 (168)
+ +.+.+|.||+|+||+.|||++.|++|||+|||||||+.||||++|+-+... +.++....|.
T Consensus 812 ~eg~d~~~~~KKk~kYaGGLVlePkkGlYe~~VLllDFNSLYPSIIQEyNICFTTv~~~~~------d~Dqlp~lP~--- 882 (1429)
T KOG0970|consen 812 EEGADEPSKGKKKAKYAGGLVLEPKKGLYEKYVLLLDFNSLYPSIIQEYNICFTTVDRFSV------DSDQLPRLPS--- 882 (1429)
T ss_pred hccccccccccccccccCceeeccccchhhheeEEEEccccchHHHHHhhheeeecccccc------CcccCCCCCC---
Confidence 1 123679999999999999999999999999999999999999999976311 2345555553
Q ss_pred EeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 127 FLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 127 f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
+...+||||++|++|++.|+++|+.||++.+|.++..|
T Consensus 883 ---s~~~~GiLPr~l~~LVerRk~VK~lMK~~~tp~~~~q~ 920 (1429)
T KOG0970|consen 883 ---SSSEQGILPRLLENLVERRKEVKKLMKQELTPEKRKQL 920 (1429)
T ss_pred ---ccccCCccHHHHHHHHHHHHHHHHHHhcCCCHHHHHhh
Confidence 23579999999999999999999999999999887654
No 7
>PHA02528 43 DNA polymerase; Provisional
Probab=99.97 E-value=2.1e-32 Score=257.90 Aligned_cols=115 Identities=25% Similarity=0.479 Sum_probs=98.3
Q ss_pred ccccccceeeeeCCCCCCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccccccccccc--------CC
Q psy12450 41 GAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITK--------LE 112 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~--------~~ 112 (168)
+.++++|+++|+.. .....+|+||+|++|+||+|++ |++|||+|||||||++|||||+|+++..+... ..
T Consensus 357 ~~~~r~g~viP~~~-~~~~~~y~Gg~V~eP~pGlY~~-VvVLDF~SLYPSIIiayNIcp~Tlv~~~~~~~~~~~~~~~~~ 434 (881)
T PHA02528 357 NSLKEEKIVIPENK-SHKKQKYAGAFVKEPVPGAYRW-VVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEYINKTAP 434 (881)
T ss_pred HHHHHcCcccCCcc-ccCCCCCCCcEEecCCCCcccc-eEEEeccccChHHHHHhCCChhhccccccccccccccccccC
Confidence 56789999999984 5566889999999999999996 99999999999999999999999998643211 11
Q ss_pred CCCCceeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCC
Q psy12450 113 LTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKET 159 (168)
Q Consensus 113 ~~~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~ 159 (168)
.+.+++..+|+|++|++. ++||+|++|++|++.|+++|++|++++
T Consensus 435 ~~~~~~~~~p~G~~F~k~--~~GiLP~iL~~Ll~~R~~~Kk~Mk~~~ 479 (881)
T PHA02528 435 RPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIYKKKMLAAE 479 (881)
T ss_pred CCCCceeEcCCCCeEeCC--CCeehHHHHHHHHHHHHHHHHHHHhcc
Confidence 334567789999999874 799999999999999999999998764
No 8
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.97 E-value=5.2e-31 Score=255.04 Aligned_cols=153 Identities=30% Similarity=0.519 Sum_probs=123.3
Q ss_pred ccccchhhhhhhhhccC----cHHHHHHHHHH---HH-HHHhccCC------CccccccceeeeeCCCC-----------
Q psy12450 2 LRHVTWRDGLETVRRDN----SPLVANMINTC---LQ-KLLINRDP------DGAVTQKNFIIPTYHGG----------- 56 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~~----c~Lv~~i~~~~---L~-~lli~r~~------~~A~~~~~~liP~~~~~----------- 56 (168)
+++|+|.|+..++|+.. .||..+|.+.+ |. .+..+|+. .|+++++||++|.+...
T Consensus 704 ~~~y~~~Da~l~~~L~~~l~~l~l~~~lt~i~G~~~~~~l~~~~~~r~e~lll~~~~~~~~i~P~~~~~~~~~~~~~~~~ 783 (1172)
T TIGR00592 704 LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQQKLGDEDE 783 (1172)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhCCcHHhccCCchHHHHHHHHHHHHHhCCEEccCccccccccccccccc
Confidence 57899999999999844 88888888887 43 33344433 38999999999986321
Q ss_pred -------CCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEee
Q psy12450 57 -------QGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLK 129 (168)
Q Consensus 57 -------~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~ 129 (168)
....+|+||+|++|++|+|++||++|||+|||||||++|||||+|+++..+. +++...| .
T Consensus 784 ~~~~~~~~~~~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~t~~~~~~~-------~~~~~~~------~ 850 (1172)
T TIGR00592 784 EIDGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDE-------DELPELP------D 850 (1172)
T ss_pred cccccccccccCcCCCeEecCCCCcccCCEEEEEcCCccHHHHHHhCcCccccCCCCcc-------hhcccCC------c
Confidence 1235799999999999999999999999999999999999999999876542 2222222 2
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 130 SSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 130 ~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
++.++||+|++|++|++.|+++|++||+++||.++++|
T Consensus 851 ~~~~~Gilp~il~~L~~~R~~~K~~mk~~~~~~~~~~~ 888 (1172)
T TIGR00592 851 SELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQY 888 (1172)
T ss_pred ccccCcchHHHHHHHHHHHHHHHHHhhcCCCHHHHHHH
Confidence 34689999999999999999999999998999988765
No 9
>PHA03036 DNA polymerase; Provisional
Probab=99.96 E-value=5.5e-30 Score=241.85 Aligned_cols=125 Identities=22% Similarity=0.424 Sum_probs=95.9
Q ss_pred cccccceeeeeCCCCCCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccccccccc-ccC---------
Q psy12450 42 AVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTI-TKL--------- 111 (168)
Q Consensus 42 A~~~~~~liP~~~~~~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~-~~~--------- 111 (168)
.+.++|+++|... .....+|+||+|+||++|+|++||++|||+|||||||++|||||||+++..+. +..
T Consensus 511 ~~~~~~~i~p~~~-~~~~~~YeGa~VlEP~~G~Y~~pV~vLDFaSLYPSIIia~NLcyeTlv~~~~~~~~~~~~i~~~~i 589 (1004)
T PHA03036 511 LLLEEKTILVRSE-TKNKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQEL 589 (1004)
T ss_pred HHHHCCcccccCC-CCccCCcCceEEecCCCCcccCCEEEEEccccchHHHHHhCCCcCeEeeccccccccccccccccc
Confidence 5667899999652 22334799999999999999988999999999999999999999999975431 100
Q ss_pred --CCCCCce---eeCCCc-----eEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 112 --ELTPDQY---SKTPCG-----NFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 112 --~~~~~~~---~~~p~~-----~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
.++..++ ...|++ ..|+.+++++||+|++|++|+++|+++|++||+++||.++++|
T Consensus 590 ~~~~p~~dy~~v~~~~~~~~~v~~~~vf~~~rkGILP~iL~~Ll~~Rk~~Kk~mK~~~d~~e~~~l 655 (1004)
T PHA03036 590 RRKYPYPRYIYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLKEATSSVEKAIY 655 (1004)
T ss_pred cccCCCccceeeeccCCcccccccceeecCCCCcChHHHHHHHHHHHHHHHHHHhhCCChHHHHHH
Confidence 1122222 223332 1344445789999999999999999999999999999998765
No 10
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Probab=99.96 E-value=1.6e-29 Score=221.45 Aligned_cols=101 Identities=34% Similarity=0.509 Sum_probs=84.9
Q ss_pred CCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcc
Q psy12450 57 QGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGL 136 (168)
Q Consensus 57 ~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gi 136 (168)
+....|+||+|++|.+|+|++||++|||+|||||||++|||||||+++..+.... ....+..|. ++++||
T Consensus 3 ~~~~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Ni~~~Ti~~~~~~~~~--------~~~~~~~~~--~~~~Gi 72 (400)
T cd05532 3 KKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDED--------DEEPPLPPS--DQEKGI 72 (400)
T ss_pred CccCCcCCceeecCCCCcccCceEEEeccccchHHHHHhcCChhhcccccccccC--------Ccccccccc--ccCCCc
Confidence 4567899999999999999999999999999999999999999999986653210 011233343 468999
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 137 LPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 137 lp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
+|++|++|++.|+++|++|++++|+.++++|
T Consensus 73 lp~~l~~l~~~R~~~K~~~k~~~d~~~~~~~ 103 (400)
T cd05532 73 LPRIIRKLVERRRQVKKLMKSEKDPDKKAQL 103 (400)
T ss_pred hHHHHHHHHHHHHHHHHHHhcCCCHHHHHHH
Confidence 9999999999999999999999999988764
No 11
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Probab=99.96 E-value=2.5e-29 Score=218.31 Aligned_cols=97 Identities=38% Similarity=0.583 Sum_probs=83.4
Q ss_pred cccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcchHH
Q psy12450 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPE 139 (168)
Q Consensus 60 ~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~ 139 (168)
++|+||+|++|.+|+|++ |++|||+|||||||++|||||||+++..+.+ .....+++++|.+ +++||+|+
T Consensus 2 ~~y~Gg~V~~P~~G~y~~-V~~lDf~SLYPSii~~~Ni~~~Ti~~~~~~~-------~~~~~~~~~~f~~--~~~Gilp~ 71 (371)
T cd05536 2 ESYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCED-------CDVEPQVGHKFRK--DPPGFIPS 71 (371)
T ss_pred CCCCceEEeCCCCCCcCC-EEEEEcccccHHHHHHHCcChhhcCCCCccc-------cccCCCCCcEEec--CCCCchHH
Confidence 569999999999999998 9999999999999999999999999876532 1222347889987 48999999
Q ss_pred HHHHHHHHHHHHHHHhccCCCh-hhhhc
Q psy12450 140 ILENLLSARKQAKNDLKKETDE-LTQVL 166 (168)
Q Consensus 140 ~L~~ll~~R~~~K~~mk~~~Dp-~~k~~ 166 (168)
+|++|++.|+++|++||+.+++ .++++
T Consensus 72 il~~ll~~R~~~K~~mk~~~~~~~~~~~ 99 (371)
T cd05536 72 VLEDLLEERRRIKEKMKKLDPESEEYKL 99 (371)
T ss_pred HHHHHHHHHHHHHHHHhhCCCcHHHHHH
Confidence 9999999999999999998765 55544
No 12
>PRK05761 DNA polymerase I; Reviewed
Probab=99.96 E-value=3.4e-29 Score=234.51 Aligned_cols=156 Identities=24% Similarity=0.352 Sum_probs=117.4
Q ss_pred ccccchhhhhhhhhcc---C---cHHHHHHHHHH---HHHHHhccCC---------CccccccceeeeeCCC----CC--
Q psy12450 2 LRHVTWRDGLETVRRD---N---SPLVANMINTC---LQKLLINRDP---------DGAVTQKNFIIPTYHG----GQ-- 57 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~---~---c~Lv~~i~~~~---L~~lli~r~~---------~~A~~~~~~liP~~~~----~~-- 57 (168)
|++|...|+..++|+. + .++.-.+...+ +..+. |.. ...++++|+++|+... ..
T Consensus 319 l~~Y~l~Da~l~~~L~~f~~~~~l~~~~elarit~lpl~~v~--r~~~g~~i~~~l~~~a~~~~~liP~~~~~~~~~~~~ 396 (787)
T PRK05761 319 LAEYNFRDAEITLKLTFFNNELVLKLILLLSRISKLPIEELS--RATISTWISNLEYWEHRKRGWLIPWKEDILRLDHEV 396 (787)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHCcCHHHHh--ccCHHHHHHHHHHHHHHhCCEeCCCCcccccccccc
Confidence 5678899999999973 2 33343343333 44442 221 2678999999999853 11
Q ss_pred ------CCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecC
Q psy12450 58 ------GEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSS 131 (168)
Q Consensus 58 ------~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~ 131 (168)
...+|+||+|++|.+|+|++ |++|||+|||||||++|||||+|+++..+.+. .+....+.++.|++
T Consensus 397 ~~~~~~~~~~y~Gg~V~~P~~G~y~~-V~vlDF~SLYPSIi~~~Ni~p~T~~~~~~~~~-----~~~~~~~~~~~~~~-- 468 (787)
T PRK05761 397 YKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETVRIPECKCH-----YDDEVPELGHSVCD-- 468 (787)
T ss_pred ccccccccCCcCCcEEeccCCCceee-EEEeeecccchHHHHHhCCChhhccCcccccc-----ccCCCCCCCceeec--
Confidence 14679999999999999999 99999999999999999999999998765321 11111245677765
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhccCC--Chhhhhcc
Q psy12450 132 LRKGLLPEILENLLSARKQAKNDLKKET--DELTQVLY 167 (168)
Q Consensus 132 ~~~Gilp~~L~~ll~~R~~~K~~mk~~~--Dp~~k~~l 167 (168)
++.||+|.+|+.|++.|+++|++|++.+ |+.++++|
T Consensus 469 ~~~gl~~~il~~l~~~R~~~k~~~~~~~~~~~~~~~~l 506 (787)
T PRK05761 469 DRPGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERRAWY 506 (787)
T ss_pred CCCCchHHHHHHHHHHHHHHHHHhhccCCCCHHHHHHH
Confidence 5899999999999999999999999754 67777654
No 13
>PRK05762 DNA polymerase II; Reviewed
Probab=99.96 E-value=1.9e-29 Score=236.36 Aligned_cols=146 Identities=25% Similarity=0.369 Sum_probs=110.6
Q ss_pred ccccchhhhhhhhhccC----cHHHHHHHHHH---HHHHHhccCC-----CccccccceeeeeCCCCCCCcccCccEeec
Q psy12450 2 LRHVTWRDGLETVRRDN----SPLVANMINTC---LQKLLINRDP-----DGAVTQKNFIIPTYHGGQGEDQFEGATVIE 69 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~~----c~Lv~~i~~~~---L~~lli~r~~-----~~A~~~~~~liP~~~~~~~~~~y~Gg~Vle 69 (168)
|.+|..+|...++++.. .|+...+...| +......... .+.++++|+++|+.. ......|+||+|++
T Consensus 330 l~~Y~l~Da~lt~~L~~kl~ll~~~~ela~l~g~~~~~v~~~~~~~e~lll~~~~~~g~v~P~~~-~~~~~~y~Gg~V~~ 408 (786)
T PRK05762 330 LARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVGGSVAAFEHLYLPRAHRAGYVAPNLG-ERPGEASPGGYVMD 408 (786)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCHHHhCccHHhHHHHHHHHHHHCCEeCCCcc-cccccccCccEEec
Confidence 35566777777776643 34444444444 2222211110 168899999999984 45568899999999
Q ss_pred ccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcchHHHHHHHHHHHH
Q psy12450 70 PKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149 (168)
Q Consensus 70 P~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~ 149 (168)
|++|+|++ |++|||+|||||||++|||||+|++...+. ++.+....++|++|++ ++||+|++|++|++.|+
T Consensus 409 p~~G~y~~-V~~lDF~SLYPSIi~~~Ni~p~T~~~~~~~-----~~~~~~~~~~~~~f~k---~~gilp~~l~~l~~~R~ 479 (786)
T PRK05762 409 SKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEGLAQ-----PPEESVAGFLGARFSR---EKHFLPEIVERLWEGRD 479 (786)
T ss_pred CCCCCcCc-eEEEEchhhhHHHHHHhCcCccceecCCCC-----CCcccccCCCCccccc---cCcchHHHHHHHHHHHH
Confidence 99999998 999999999999999999999999866542 1223456778999965 79999999999999999
Q ss_pred HHHHHhcc
Q psy12450 150 QAKNDLKK 157 (168)
Q Consensus 150 ~~K~~mk~ 157 (168)
++|++|++
T Consensus 480 ~~K~~~~~ 487 (786)
T PRK05762 480 EAKREMNK 487 (786)
T ss_pred HHHHHHHH
Confidence 99999986
No 14
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=99.95 E-value=7.3e-30 Score=226.49 Aligned_cols=126 Identities=36% Similarity=0.655 Sum_probs=95.5
Q ss_pred ccccccceeeeeCCCC--------CCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccccccc-cc-cc
Q psy12450 41 GAVTQKNFIIPTYHGG--------QGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQ-TI-TK 110 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~--------~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~-~~-~~ 110 (168)
+.++++|+++|+.... .....|+||+|++|.+|+|+++|.+|||+|||||||++|||||||+++.. +. +.
T Consensus 12 ~~~~~~~~~~p~~~~~~~~~~~~~~~~~~y~Gg~V~~P~~G~~~~v~~~lDF~SLYPsii~~~Ni~~~T~~~~~~~~~~~ 91 (466)
T PF00136_consen 12 REAHRRNYIIPSKKERPEGFTSKSEQKEKYEGGYVLEPKPGLYENVVSVLDFASLYPSIIIAYNICPETIVDDDECKDNE 91 (466)
T ss_dssp HHHHHTTBE-B-HHHHHHTHHHHHHHCTCEEEC-BE--HSSEEEEEEEEEEETTHHHHHHHHTTHSTTTBTCTTHCSSEE
T ss_pred HHHHHCCEEeeCCcccccccccccccccccccceeeccccccccCceeeeecccccHHHHHhccCCcceEecchhhhccc
Confidence 4578899999997532 24678999999999999999955589999999999999999999999986 11 11
Q ss_pred C--C--CCCCc-eeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhh-hhc
Q psy12450 111 L--E--LTPDQ-YSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELT-QVL 166 (168)
Q Consensus 111 ~--~--~~~~~-~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~-k~~ 166 (168)
. . .+... ....+.+..|+....++|++|++|+.+++.|+++|++|++++|+.+ +++
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gilp~~l~~~l~~R~~~K~~~~~~~~~~~~~~~ 153 (466)
T PF00136_consen 92 VSPDIKYDYGPFIVGSPVGVRFVKKGVRPGILPEILEELLEKRKEIKKLMKKAKDPDEEYAI 153 (466)
T ss_dssp EHTTCCCCTCEEEECSCCSEEEESSTCSHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_pred ccccccccccceeecCCceeeecccCcccccChHHHHHHHHHHHHHhhhhhhhccchhhHHH
Confidence 1 0 01111 1234566789888899999999999999999999999999988876 544
No 15
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=99.95 E-value=2.1e-28 Score=209.02 Aligned_cols=99 Identities=42% Similarity=0.661 Sum_probs=81.0
Q ss_pred cccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcchHH
Q psy12450 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPE 139 (168)
Q Consensus 60 ~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~ 139 (168)
++|+||+|++|.+|+|++ |++|||+|||||||++|||||+|+++..+... .++ +.+..|..+.+++||+|.
T Consensus 1 ~~y~Gg~V~~P~~G~~~~-V~~lDf~SLYPSIi~~~Ni~~~T~~~~~~~~~----~~~----~~~~~~~~~~~~~Gilp~ 71 (323)
T cd00145 1 EPYEGGYVFDPIPGLYEN-VIVLDFKSLYPSIIITYNLSPTTLVGNGEIAA----PED----YIGVGFRSPKDRKGLLPR 71 (323)
T ss_pred CCCCCcEEecCcccccCc-eEEeecCCccHHHHHHhCCCcccccccccccC----ccc----ccCccccccCCCCCCCHH
Confidence 469999999999999996 99999999999999999999999998755321 111 113334444578999999
Q ss_pred HHHHHHHHHHHHHHHhccCCC-hhhhhcc
Q psy12450 140 ILENLLSARKQAKNDLKKETD-ELTQVLY 167 (168)
Q Consensus 140 ~L~~ll~~R~~~K~~mk~~~D-p~~k~~l 167 (168)
+|++|++.|+++|++|++++| +.++++|
T Consensus 72 iL~~Ll~~R~~~K~~mk~~~~~~~~~~~~ 100 (323)
T cd00145 72 ILEELLNFRDEAKKRMKAAKLAPEERVLY 100 (323)
T ss_pred HHHHHHHHHHHHHHHHhhCcCCHHHHHHH
Confidence 999999999999999999875 8777654
No 16
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=99.95 E-value=1.9e-28 Score=229.84 Aligned_cols=116 Identities=38% Similarity=0.640 Sum_probs=97.6
Q ss_pred ccccccceeeeeCCCCCCC-cccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCcee
Q psy12450 41 GAVTQKNFIIPTYHGGQGE-DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~~~~-~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~ 119 (168)
+.+++.|+++|++. .... ..|+||+|++|.+|+|++ |++|||+|||||||++|||||+|+++.++. +...
T Consensus 385 ~~a~~~~~~iP~~~-~~~~~~~~~Gg~V~~P~~Gly~~-V~vLDF~SLYPSII~~~Ni~p~T~~~~~~~-------~~~~ 455 (792)
T COG0417 385 REAKRRGELIPNKE-ERPERKKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDTLVEEDCS-------DDYS 455 (792)
T ss_pred HHHhhcCEeccCcc-ccchhhhcCCCEEccCCccccCc-EEEEEccccChHHHHHhCCCcceecCCCcc-------cccc
Confidence 68899999999995 4444 689999999999999999 999999999999999999999999987753 1222
Q ss_pred eCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 120 ~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
....++.| ++.++|++|++|++|++.|.++|++|++++|+.++.+|
T Consensus 456 ~~~~~~~~--~~~~~G~lp~il~~L~~~R~~~K~~~k~~~~~~e~~~~ 501 (792)
T COG0417 456 PPGVGHGF--CKREKGFLPEILEELLDRRDEIKKKMKKEKDPSERKLL 501 (792)
T ss_pred CCCCcccc--cccCCCchHHHHHHHHHHHHHHHHHhcccCChHHHHHH
Confidence 22233444 34689999999999999999999999999999887665
No 17
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=99.95 E-value=4.5e-28 Score=210.58 Aligned_cols=99 Identities=32% Similarity=0.576 Sum_probs=80.0
Q ss_pred CcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCC-CceEEeecCCCCcch
Q psy12450 59 EDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTP-CGNFFLKSSLRKGLL 137 (168)
Q Consensus 59 ~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p-~~~~f~~~~~~~Gil 137 (168)
..+|+||+|++|++|+|++ |++|||+|||||||++|||||||++++.+.+ .. ...| .+++|.+ +++||+
T Consensus 10 ~~~y~Gg~V~~P~~G~y~~-V~~lDF~SLYPSIi~~~Ni~~~T~~~~~~~~------~~-~~~p~~~~~~~~--~~~Gil 79 (372)
T cd05530 10 GKKYRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCEC------KT-NEVPEVGHWVCK--KRPGIT 79 (372)
T ss_pred CCCCCCCEeecCCCCcccc-EEEEEcccccHHHHHHhCCChhhcccCcccc------cc-eecCCCCceEEe--cCCCcc
Confidence 4679999999999999999 9999999999999999999999999875432 12 2234 3455544 589999
Q ss_pred HHHHHHHHHHHHHHHHHh-ccCC-Chhhhhcc
Q psy12450 138 PEILENLLSARKQAKNDL-KKET-DELTQVLY 167 (168)
Q Consensus 138 p~~L~~ll~~R~~~K~~m-k~~~-Dp~~k~~l 167 (168)
|++|+.|++.|+++|++| ++++ ||.++++|
T Consensus 80 p~il~~L~~~R~~~~k~~~k~~~~d~~~~~~l 111 (372)
T cd05530 80 SQIIGLLRDLRVKIYKKKAKDKSLDEEMRQWY 111 (372)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH
Confidence 999999999999875555 4455 88888664
No 18
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=99.94 E-value=7.7e-27 Score=201.62 Aligned_cols=91 Identities=33% Similarity=0.473 Sum_probs=78.0
Q ss_pred cccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcchHH
Q psy12450 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPE 139 (168)
Q Consensus 60 ~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~ 139 (168)
.+|+||+|++|.+|+|++ |++|||+|||||||++|||||+|+++.++... ...+.++.|.+ +++||+|+
T Consensus 3 ~~~~Gg~V~~p~~G~~~~-V~~lDF~SLYPSii~~~ni~~~ti~~~~~~~~--------~~~~~~~~~~~--~~~gilp~ 71 (352)
T cd05531 3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCRCCECR--------DHVYLGHRICL--KRRGFLPE 71 (352)
T ss_pred cCCCCcEEecCCCCccCc-eEEEEccccchHHHHHhCCChhhccccCcccc--------cCCCCCceEec--CCCCchHH
Confidence 469999999999999998 99999999999999999999999987654321 11245666655 58999999
Q ss_pred HHHHHHHHHHHHHHHhccCCCh
Q psy12450 140 ILENLLSARKQAKNDLKKETDE 161 (168)
Q Consensus 140 ~L~~ll~~R~~~K~~mk~~~Dp 161 (168)
+|++|++.|.++|++||+++++
T Consensus 72 ~l~~l~~~R~~~K~~~k~~~~~ 93 (352)
T cd05531 72 VLEPLLERRLEYKRLKKEEDPY 93 (352)
T ss_pred HHHHHHHHHHHHHHHhhcCCCc
Confidence 9999999999999999987654
No 19
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=99.94 E-value=5.1e-27 Score=224.00 Aligned_cols=109 Identities=24% Similarity=0.300 Sum_probs=82.5
Q ss_pred CcccCccEeecccCcc-----ccCCeEEeecCCcChhHHHhhcCCccccccccccccC-CCCCCceeeCCCc--------
Q psy12450 59 EDQFEGATVIEPKKGY-----YADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKL-ELTPDQYSKTPCG-------- 124 (168)
Q Consensus 59 ~~~y~Gg~VleP~~G~-----y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~-~~~~~~~~~~p~~-------- 124 (168)
..+|+||+|++|.+|+ |.+||++|||+|||||||++|||||||++++.+.+.. +....++...|.+
T Consensus 630 ~~~YeGAtVLEP~~Gf~~~~~Y~~PVaVLDFASLYPSIIiahNLCYeTLV~~~c~~~~~~~~~~d~~k~p~gy~~~~~vy 709 (1545)
T PHA03334 630 KIKLKGGYVFAPLTGLTFAGPYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTARVRGWVVFDWKKIDRGFGKATLMY 709 (1545)
T ss_pred ccccCCeEeecCCCCccccccCCCcEEEEEccccchHHHHHhCCCcccccCccchhhhccccccccccCCcccCccccce
Confidence 4579999999999999 5679999999999999999999999999987654221 1111111111111
Q ss_pred ------eEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 125 ------NFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 125 ------~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
..+...+...+++|++|++||++|+++|++||+++||.+|.+|
T Consensus 710 ~V~~~~~~~P~~~rf~SiLp~LL~eLL~~RK~~Kk~MKk~kDp~er~iL 758 (1545)
T PHA03334 710 TILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQAKDPKLKSYH 758 (1545)
T ss_pred eeccccCcCCCcceecchHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHH
Confidence 1122223456899999999999999999999999999988775
No 20
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=99.93 E-value=1.8e-26 Score=200.49 Aligned_cols=89 Identities=29% Similarity=0.486 Sum_probs=76.8
Q ss_pred ccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcchHHH
Q psy12450 61 QFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEI 140 (168)
Q Consensus 61 ~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~~ 140 (168)
+++||+|++|++|+|++ |++|||+|||||||++|||||+|++...+.. +.++....+++.+|++ ++||+|++
T Consensus 2 ~~~Gg~V~eP~~G~y~~-V~vlDF~SLYPSII~~~Ni~p~t~~~~~~~~----~~~~~~~~~~~~~f~~---~~Gilp~~ 73 (371)
T cd05537 2 SSPGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGLKAP----DPEDLIPGFLGARFSR---EKHILPDL 73 (371)
T ss_pred CCCCcEEeCCCCCccCc-eEEEEcccccHHHHHHhCCCCceecCCCCCC----CccccccCCCCCeEec---CCCchHHH
Confidence 47899999999999998 9999999999999999999999998765421 1234566778889987 35999999
Q ss_pred HHHHHHHHHHHHHHhcc
Q psy12450 141 LENLLSARKQAKNDLKK 157 (168)
Q Consensus 141 L~~ll~~R~~~K~~mk~ 157 (168)
|++|++.|+++|++|++
T Consensus 74 l~~l~~~R~~~K~~~~~ 90 (371)
T cd05537 74 IARLWAARDEAKREKNA 90 (371)
T ss_pred HHHHHHHHHHHHHhccH
Confidence 99999999999998764
No 21
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=99.92 E-value=2.1e-25 Score=194.24 Aligned_cols=122 Identities=42% Similarity=0.741 Sum_probs=98.5
Q ss_pred ccccccceeeeeCCCCC---------CCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccccccccccc-
Q psy12450 41 GAVTQKNFIIPTYHGGQ---------GEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITK- 110 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~~---------~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~- 110 (168)
+.+++.|+++|...... ...+|+||+|++|.+|+|++||+++||+|||||||++|||||+|+++..+...
T Consensus 255 ~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~y~gg~v~~p~~g~~~~~v~~lDf~SlYPsii~~~nl~~~t~~~~~~~~~~ 334 (471)
T smart00486 255 REAKKNNYILPSKSLIDFKGSEPELKKKAKYPGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGRGENSGE 334 (471)
T ss_pred HHHhhCCEEeccchhcccccccccccccccccccEEecCCCCcccCceEEeehhhccHHHHHHhCCCCcccccccccccc
Confidence 68889999999875422 24679999999999999999999999999999999999999999998764211
Q ss_pred CCCCC----CceeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChh
Q psy12450 111 LELTP----DQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDEL 162 (168)
Q Consensus 111 ~~~~~----~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~ 162 (168)
..... ......+.+..|.+++.+.|++|++|++|++.|.++|+.|++++|+.
T Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~gil~~~l~~l~~~R~~~K~~~~~~~~~~ 390 (471)
T smart00486 335 LFLDVEDLLTIKYEKPEGYHFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDES 390 (471)
T ss_pred cCCChhhcceeeecCCCcceeecCCCCCeehHHHHHHHHHHHHHHHHHHhhCCCCc
Confidence 00000 11234567778888777789999999999999999999999987665
No 22
>KOG0968|consensus
Probab=99.91 E-value=1.3e-25 Score=210.82 Aligned_cols=126 Identities=35% Similarity=0.589 Sum_probs=102.0
Q ss_pred ccccccceeeeeCCCCCCCc--ccC-ccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccccccccc-----c-cC
Q psy12450 41 GAVTQKNFIIPTYHGGQGED--QFE-GATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTI-----T-KL 111 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~~~~~--~y~-Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~-----~-~~ 111 (168)
--++.+||+.|++...+... +-+ =.+||||++.||.+||+||||+|||||||||||+||+|+.+.... + ++
T Consensus 923 RiAk~~Nyi~~SPs~kQv~~q~A~EcvPLVMEPeS~fY~~PViVLDFQSLYPSivIAYNyCySTcLG~v~~l~~~~e~~L 1002 (1488)
T KOG0968|consen 923 RIAKPMNYIAPSPSHKQVAMQGAPECVPLVMEPESAFYFDPVIVLDFQSLYPSIVIAYNYCYSTCLGKVGNLNQMNEIKL 1002 (1488)
T ss_pred HHhcccccccCCccHHHHhhcCCccccceeecchhhhccCceEEEEchhhcchHHHhHHHHHHHhhhHHHhhccccceee
Confidence 47889999999985322211 112 358999999999999999999999999999999999999877543 0 12
Q ss_pred C-----CC-------CCceeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCC-Chhhhhc
Q psy12450 112 E-----LT-------PDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKET-DELTQVL 166 (168)
Q Consensus 112 ~-----~~-------~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~-Dp~~k~~ 166 (168)
| ++ .+++..+|+|+.|+++++|+|+||++|+++|+.|-.+|+.||+.+ +...+.+
T Consensus 1003 G~s~~s~~~dil~~~~ndV~isPNgv~yVK~sVRkgvLpkmLeEIL~tRiMVKkaMK~~~~~~~L~Ri 1070 (1488)
T KOG0968|consen 1003 GVSKYSLPPDILVLAKNDVTISPNGVMYVKPSVRKGVLPKMLEEILATRIMVKKAMKRTKDNKKLKRI 1070 (1488)
T ss_pred eeeeccCCHHHHHHHhcceeeCCCceEEechhhhhhhHHHHHHHHHHHHHHHHHHHHHhcchHHHHHH
Confidence 2 22 357889999999999999999999999999999999999999987 4444443
No 23
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=99.90 E-value=2e-24 Score=186.26 Aligned_cols=76 Identities=28% Similarity=0.420 Sum_probs=70.2
Q ss_pred ccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecCCCCcchHHH
Q psy12450 61 QFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEI 140 (168)
Q Consensus 61 ~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~~ 140 (168)
+|+||+|++|.||+|++ |++|||+|||||||++|||||+. ++.||+|++
T Consensus 2 ~~~GG~v~~p~~Gl~~~-V~~lDf~SLYPSIi~~~ni~p~~------------------------------~~~Gilp~i 50 (347)
T cd05538 2 KFEGGYAYVFITGVLGP-IVHADVASLYPSIMLAYRICPAR------------------------------DSLGIFLAL 50 (347)
T ss_pred CcCCceEcccCCcCcCc-eEEEEcccchHHHHHHhCCCCCC------------------------------CCCcccHHH
Confidence 68999999999999998 99999999999999999999841 258999999
Q ss_pred HHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 141 LENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 141 L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
|++|++.|+++|++||+++||.++.+|
T Consensus 51 l~~Ll~~R~~~K~~~k~~~~~~~~~~~ 77 (347)
T cd05538 51 LKYLVELRLAAKESARAAARPAERDAF 77 (347)
T ss_pred HHHHHHHHHHHHHHHhcCCChHHHHHH
Confidence 999999999999999999999887664
No 24
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.19 E-value=2.8e-12 Score=125.24 Aligned_cols=131 Identities=26% Similarity=0.377 Sum_probs=90.0
Q ss_pred HHHHHhccCCCccccccceeeeeCCCC-----CCCcccCccEeecc--cCccccC--CeEEeecC--CcChhHHHhhcCC
Q psy12450 30 LQKLLINRDPDGAVTQKNFIIPTYHGG-----QGEDQFEGATVIEP--KKGYYAD--PIATLDFS--SLYPSIMMAHNLC 98 (168)
Q Consensus 30 L~~lli~r~~~~A~~~~~~liP~~~~~-----~~~~~y~Gg~VleP--~~G~y~~--pV~~lDF~--SLYPSIm~~~Ni~ 98 (168)
+..+++.|- +...+.+.|..... ..+.+|+|+.|++| .+|+|.+ |+++|||+ |||||||++||||
T Consensus 452 ~erfll~rk----i~gp~WL~i~~p~~~~~~~~S~c~yEga~v~~p~v~~g~~~~~pPl~vLdFsi~SlyPsi~~~~nl~ 527 (1172)
T TIGR00592 452 LERFLLLRK----IKGPCWLAVKGPDELEYPRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVS 527 (1172)
T ss_pred HHHHHhcCC----CCCCceEEeCCCcccCcCCccccceEEEEecCccccccccCCCCCeEEEEeeeEEecCccccCceEE
Confidence 455666543 66666666643211 23567999999999 9999998 89999999 9999999999999
Q ss_pred ccccccccccccCCCCCCc-eeeCCC-ceEEeec-------CCCCcchHHHHHHHHHHHHHHHHHhccCC--Chhhhh
Q psy12450 99 YTTLLTPQTITKLELTPDQ-YSKTPC-GNFFLKS-------SLRKGLLPEILENLLSARKQAKNDLKKET--DELTQV 165 (168)
Q Consensus 99 p~Tl~~~~~~~~~~~~~~~-~~~~p~-~~~f~~~-------~~~~Gilp~~L~~ll~~R~~~K~~mk~~~--Dp~~k~ 165 (168)
++|++....... +.++++ +...++ +.+|... ...+|++|..|+.++++|+.+++.|+... ||....
T Consensus 528 iS~~v~~~~~~d-~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~ 604 (1172)
T TIGR00592 528 IPDTLHREFALD-KPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIV 604 (1172)
T ss_pred EEEEEeeccccc-CCCCCCccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEE
Confidence 888875432100 111111 211111 1223111 14679999999999999999999999876 876554
No 25
>KOG0969|consensus
Probab=98.23 E-value=4.7e-07 Score=84.59 Aligned_cols=34 Identities=65% Similarity=1.026 Sum_probs=31.9
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCCCc
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDPDG 41 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~~~ 41 (168)
.||+|||||||||||.++++.||+++|++|++.+
T Consensus 789 ~kGietVRRDnc~LV~~v~~~~L~kiLi~rdv~g 822 (1066)
T KOG0969|consen 789 CKGIETVRRDNCPLVANVVNTVLRKILIERDVEG 822 (1066)
T ss_pred ccccchhccCCchHHHHHHHHHHHHHHhhcChHH
Confidence 4899999999999999999999999999999853
No 26
>PHA02563 DNA polymerase; Provisional
Probab=97.58 E-value=3.4e-05 Score=71.70 Aligned_cols=42 Identities=21% Similarity=0.301 Sum_probs=37.8
Q ss_pred CcccCccEee---cccCccccCCeEEeecCCcChhHHHhhcCCccc
Q psy12450 59 EDQFEGATVI---EPKKGYYADPIATLDFSSLYPSIMMAHNLCYTT 101 (168)
Q Consensus 59 ~~~y~Gg~Vl---eP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~T 101 (168)
..+|.||.|+ ++.+|++++ +.++|++|||||+|...++++.+
T Consensus 235 r~sY~GGr~~~~~~~~~~~~~~-~~~yDvnSlYPsaM~~~~~P~g~ 279 (630)
T PHA02563 235 RKFYRGGRTWYNPKYIGKLIEE-GYVYDVNSLYPYVMYNAKLPYGE 279 (630)
T ss_pred HHheeCceeecccccccccccc-ccccccccccHHHHhhccCCCCC
Confidence 3579999998 889999988 77999999999999999998875
No 27
>KOG0968|consensus
Probab=97.23 E-value=0.00016 Score=70.20 Aligned_cols=32 Identities=41% Similarity=0.679 Sum_probs=29.7
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
+|||||||||.||.|++|+.+||+-|+-+++-
T Consensus 1206 AKGIETVRRDtcPavakilEksL~LlFetkdl 1237 (1488)
T KOG0968|consen 1206 AKGIETVRRDTCPAVAKILEKSLRLLFETKDL 1237 (1488)
T ss_pred cccceeeeccCcHHHHHHHHHHHHHHhhcccH
Confidence 69999999999999999999999988888873
No 28
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=95.98 E-value=0.0024 Score=62.83 Aligned_cols=32 Identities=53% Similarity=0.800 Sum_probs=29.9
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||+|+||||+|++++++++++|..+|.+++.
T Consensus 783 ~KGie~vRRD~c~~~k~~~~~vl~~il~~~d~ 814 (1054)
T PTZ00166 783 CKGIETVRRDNCLLVQQMVETVLNKILIEKDV 814 (1054)
T ss_pred eeeeEEEeccchHHHHHHHHHHHHHHHccCCH
Confidence 68999999999999999999999999988775
No 29
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins. Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.
Probab=95.60 E-value=0.0039 Score=55.64 Aligned_cols=35 Identities=31% Similarity=0.330 Sum_probs=25.2
Q ss_pred CCcccCccEeecccCccccCCeEEeecCCcChhHHH
Q psy12450 58 GEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMM 93 (168)
Q Consensus 58 ~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~ 93 (168)
..++|-||.+..-.+|... ++..+|++|||||+|.
T Consensus 202 ir~s~~GGr~~~~~~~~~~-~i~~yDvnSLYP~~m~ 236 (459)
T PF03175_consen 202 IRKSYYGGRCEVFKPGIKN-KIYYYDVNSLYPSAMK 236 (459)
T ss_dssp --EEE-GGGB-TEEEESE----EEEEETTHHHHHHH
T ss_pred HHhhcCCceeeeeeccccc-ceeeeeccCCcHHHHh
Confidence 3567899998777778777 5999999999999998
No 30
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=93.44 E-value=0.046 Score=46.94 Aligned_cols=29 Identities=41% Similarity=0.605 Sum_probs=27.2
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhc
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLIN 36 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~ 36 (168)
.||++++|||+|++++++...++..++.+
T Consensus 229 ~KG~e~vRrD~~~~~k~~~~~vl~~ll~~ 257 (323)
T cd00145 229 IKGLETRRRDSPPLVKKFQKEVLELILEE 257 (323)
T ss_pred EEcceEEecCcHHHHHHHHHHHHHHHHcC
Confidence 48999999999999999999999999984
No 31
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=93.42 E-value=0.04 Score=48.34 Aligned_cols=32 Identities=28% Similarity=0.412 Sum_probs=29.6
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||++++|||+|+++.++.+.++..++.+.++
T Consensus 236 ~KGle~vRrD~~~l~k~~~~~vl~~il~~~~~ 267 (371)
T cd05537 236 FKGLETVRSDWTPLARQFQKELYERVFNDEPY 267 (371)
T ss_pred eecceeEecchHHHHHHHHHHHHHHHhcCCCH
Confidence 48999999999999999999999999988765
No 32
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=93.41 E-value=0.05 Score=48.03 Aligned_cols=32 Identities=59% Similarity=0.965 Sum_probs=29.3
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||++++|||.|++++++..+++..+|.+.++
T Consensus 245 ~KGle~vRRD~~~~~k~~~~~vl~~il~~~~~ 276 (393)
T cd05533 245 TKGIETVRRDNCLLVQNVVETCLNKILIERDV 276 (393)
T ss_pred EeceEEEcccchHHHHHHHHHHHHHHHhcCCH
Confidence 48999999999999999999999999977764
No 33
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Probab=93.37 E-value=0.047 Score=49.11 Aligned_cols=32 Identities=38% Similarity=0.651 Sum_probs=29.3
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||+++||||.|++++++.++++..+|.+.+.
T Consensus 297 ~KGle~vRrD~~~~~k~~~~~vl~~il~~~d~ 328 (451)
T cd05534 297 AKGIETVRRDGCPAVQKILEKSLRILFETKDL 328 (451)
T ss_pred eecceEEecccHHHHHHHHHHHHHHHhccCCH
Confidence 47999999999999999999999999977764
No 34
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=93.32 E-value=0.042 Score=47.88 Aligned_cols=32 Identities=31% Similarity=0.528 Sum_probs=29.4
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||++++|||+|++++++...++..++.++++
T Consensus 215 ~KG~e~vRrD~~~~~k~~~~~vl~~ll~~~~~ 246 (352)
T cd05531 215 VRGIELRRRDTPPFVKKFQEEALDILASAKTP 246 (352)
T ss_pred EEeeEEEeCCchHHHHHHHHHHHHHHhcCCCH
Confidence 48999999999999999999999999987775
No 35
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=93.05 E-value=0.046 Score=50.85 Aligned_cols=29 Identities=24% Similarity=0.542 Sum_probs=26.4
Q ss_pred eEEeecCCcChhHHHhhcCCccccccccc
Q psy12450 79 IATLDFSSLYPSIMMAHNLCYTTLLTPQT 107 (168)
Q Consensus 79 V~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~ 107 (168)
|..||.+||||+||.+.-+-|++++....
T Consensus 92 IYHlDV~aMYpnIiltnRLQP~a~v~e~~ 120 (621)
T cd05535 92 IYHLDVAAMYPNIILTNRLQPDAIVDEDV 120 (621)
T ss_pred eeEeehhhccchhhhhccCCCcccCCHHh
Confidence 78999999999999999999999987643
No 36
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Probab=92.72 E-value=0.065 Score=46.94 Aligned_cols=32 Identities=34% Similarity=0.398 Sum_probs=29.1
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||++++|||+|++++++.+.++..++.+.+.
T Consensus 221 ~KG~e~~RrD~~~~~k~~~~~~l~~ll~~~~~ 252 (371)
T cd05536 221 VVGLEVVRRDWSEIAKETQARVLEAILKEGDV 252 (371)
T ss_pred EEeeeeEeCccHHHHHHHHHHHHHHHHcCCCH
Confidence 58999999999999999999999999976664
No 37
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Probab=92.53 E-value=0.052 Score=48.03 Aligned_cols=32 Identities=34% Similarity=0.543 Sum_probs=29.2
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||++++|||+|+++.++.+.++..++-+.++
T Consensus 233 ~KGie~~RrD~~~~~k~~~~~vl~~ll~~~~~ 264 (400)
T cd05532 233 VKGLDIVRRDWCPLSKEIGNYVLDQILSDKSR 264 (400)
T ss_pred EeceeEEecccHHHHHHHHHHHHHHHHcCCCh
Confidence 58999999999999999999999999977764
No 38
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=91.63 E-value=0.12 Score=44.95 Aligned_cols=28 Identities=18% Similarity=0.298 Sum_probs=25.9
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHh
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLI 35 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli 35 (168)
.||+++||||+|+++.++..+++..++-
T Consensus 200 ~KG~e~vRrD~~~~~k~~~~~vl~~ll~ 227 (347)
T cd05538 200 VKGSAFRSRGIEPFLREFLREAVRLLLQ 227 (347)
T ss_pred EECCCcccCCchHHHHHHHHHHHHHHHc
Confidence 5899999999999999999999988773
No 39
>PHA03036 DNA polymerase; Provisional
Probab=91.44 E-value=0.11 Score=51.08 Aligned_cols=31 Identities=29% Similarity=0.387 Sum_probs=26.7
Q ss_pred hhhhhhhhccCcHHHHHHHHHH---HHHHHhccC
Q psy12450 8 RDGLETVRRDNSPLVANMINTC---LQKLLINRD 38 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~---L~~lli~r~ 38 (168)
.||+++||||+|+++.+++++. |..+|.+++
T Consensus 827 ~KGie~VRRD~c~fvK~v~~~vi~~L~~iL~~~d 860 (1004)
T PHA03036 827 NKGTSETRRDVSKFHKYMIKIYKTRLLDMLSEGN 860 (1004)
T ss_pred EECceeEeCchHHHHHHHHHHHHHHHHHHhccCC
Confidence 6899999999999999999996 456677775
No 40
>PHA02528 43 DNA polymerase; Provisional
Probab=91.43 E-value=0.11 Score=50.37 Aligned_cols=30 Identities=20% Similarity=0.411 Sum_probs=27.7
Q ss_pred hhhhhhhccCcHHHHHHHHHHHHHHHhccC
Q psy12450 9 DGLETVRRDNSPLVANMINTCLQKLLINRD 38 (168)
Q Consensus 9 ~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~ 38 (168)
+|+|+||+|.|||++++..+++..+|.+..
T Consensus 706 kGlEtvRsD~~~lak~~q~~vi~~Il~~~~ 735 (881)
T PHA02528 706 MGIETQRSSTPKAVQKALKEAIRRILQEGE 735 (881)
T ss_pred ecceeeecchHHHHHHHHHHHHHHHHhCCc
Confidence 899999999999999999999999998743
No 41
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=91.30 E-value=0.085 Score=50.58 Aligned_cols=35 Identities=46% Similarity=0.566 Sum_probs=32.6
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCCCcc
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDPDGA 42 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~~~A 42 (168)
.||++++|||.|||+.++..+|+..++.++++..+
T Consensus 628 vKG~e~~RrD~~~l~k~~q~~vl~~il~~~~~e~~ 662 (792)
T COG0417 628 VKGLETVRRDWPELVKEFQREVLEVLLSGRDVEEA 662 (792)
T ss_pred EeeeEEEecCccHHHHHHHHHHHHHHHcCCCHHHH
Confidence 47999999999999999999999999999998766
No 42
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=91.06 E-value=0.19 Score=44.96 Aligned_cols=33 Identities=39% Similarity=0.677 Sum_probs=30.1
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDPD 40 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~~ 40 (168)
.+|++++|||+|+++.++...++..++.+.++.
T Consensus 288 ~kG~e~~RrD~~~~~k~~~~~~l~~il~~~~~~ 320 (466)
T PF00136_consen 288 IKGLELVRRDWCPFVKDIQREVLEIILKGKDPE 320 (466)
T ss_dssp EESSSGGSSSSTHHHHHHHHHHHHHHHTTCCHH
T ss_pred EeccccccCchhHHHHHHHHHHHHHHhCCCCHH
Confidence 489999999999999999999999998888764
No 43
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=90.90 E-value=0.13 Score=45.17 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=28.3
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||++++|||+|+++.++...++..++...++
T Consensus 229 ~KGie~~RrD~~~~~k~~~~~vl~~ll~~~~~ 260 (372)
T cd05530 229 IKGLLGKKRNTPEFVKELFYEVIEILSAVNSP 260 (372)
T ss_pred EEeEEEEeCCchHHHHHHHHHHHHHHHhcCCh
Confidence 58999999999999999999999888876553
No 44
>PHA02735 putative DNA polymerase type B; Provisional
Probab=90.55 E-value=0.15 Score=46.09 Aligned_cols=42 Identities=26% Similarity=0.361 Sum_probs=34.5
Q ss_pred CcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccc
Q psy12450 59 EDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTL 102 (168)
Q Consensus 59 ~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl 102 (168)
++.|-||.+-.-++|=+.. |+.-|.+|+||+||... =.|.|+
T Consensus 269 wEsYyGGrfeV~KrgnvGE-v~~pDINSaYPaim~dl-PDpKTl 310 (716)
T PHA02735 269 WESYAGGRFEVFKRGNVGE-VAAPDINSAYPAILADL-PDPKTL 310 (716)
T ss_pred HHhhcCCceEEeccCccce-eeeccccccchHHHHhC-CCCccc
Confidence 4678999877778898887 99999999999999983 356664
No 45
>PRK05761 DNA polymerase I; Reviewed
Probab=90.33 E-value=0.15 Score=49.05 Aligned_cols=33 Identities=21% Similarity=0.388 Sum_probs=30.2
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDPD 40 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~~ 40 (168)
.||++++|||.|+++.++...++..++.++++.
T Consensus 624 ~KG~e~vRrD~~~~~k~~~~~vl~~ll~~~~~~ 656 (787)
T PRK05761 624 IKGIVAKKRNTPEFVKELQREVLEVLKSIRSPE 656 (787)
T ss_pred EEEEEEEeCCchHHHHHHHHHHHHHHhcCCChh
Confidence 489999999999999999999999999887754
No 46
>PRK05762 DNA polymerase II; Reviewed
Probab=87.50 E-value=0.29 Score=46.97 Aligned_cols=32 Identities=28% Similarity=0.411 Sum_probs=29.3
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||+++||||.|+++.++...++..++.+.++
T Consensus 634 ~KGle~vRrD~~~~~k~~~~~vl~~il~~~~~ 665 (786)
T PRK05762 634 FKGLETVRTDWTPLAKEFQQELYERIFRGEPY 665 (786)
T ss_pred EEeeEEECCChHHHHHHHHHHHHHHHhcCCCH
Confidence 48999999999999999999999999988774
No 47
>KOG1798|consensus
Probab=77.50 E-value=0.82 Score=46.79 Aligned_cols=28 Identities=25% Similarity=0.581 Sum_probs=25.9
Q ss_pred eEEeecCCcChhHHHhhcCCcccccccc
Q psy12450 79 IATLDFSSLYPSIMMAHNLCYTTLLTPQ 106 (168)
Q Consensus 79 V~~lDF~SLYPSIm~~~Ni~p~Tl~~~~ 106 (168)
|..||.+||||+||.+.-+-|.+++...
T Consensus 598 IYHLDVaaMYPNIilTNRLQP~siv~E~ 625 (2173)
T KOG1798|consen 598 IYHLDVAAMYPNIILTNRLQPDSIVDEE 625 (2173)
T ss_pred EEEEehhhccCceeeecCCCCcccccHh
Confidence 7899999999999999999999998764
No 48
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=71.26 E-value=1.6 Score=40.84 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=30.1
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDPD 40 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~~ 40 (168)
.||+|.+|||.|+|+.++-+.++..+|.+.+.+
T Consensus 436 lKGfEikRRd~~~LaK~fQ~eV~e~iL~g~~~E 468 (621)
T cd05535 436 LKGFEVKRRGELQLIKIFQSEVFDAFLKGSTLE 468 (621)
T ss_pred EeCceeeeCCHHHHHHHHHHHHHHHHHcCCCHH
Confidence 489999999999999999999999999888754
No 49
>KOG0970|consensus
Probab=52.74 E-value=11 Score=38.00 Aligned_cols=31 Identities=32% Similarity=0.523 Sum_probs=28.2
Q ss_pred hhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 9 DGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 9 ~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
||+-.||||-|+|+..+-..||..+|.+.+.
T Consensus 1051 KGLDmvRRDwc~Lake~g~~vLd~ILs~~~~ 1081 (1429)
T KOG0970|consen 1051 KGLDMVRRDWCQLAKEIGKAVLDKILSDKSR 1081 (1429)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHHHcCCCH
Confidence 7999999999999999999999999877664
No 50
>PF08988 DUF1895: Protein of unknown function (DUF1895); InterPro: IPR015081 The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The function of this protein is, as yet, unknown. ; PDB: 1ZW0_B 2P58_A 2UWJ_E 2Q1K_D 3PH0_B.
Probab=49.96 E-value=25 Score=23.63 Aligned_cols=31 Identities=19% Similarity=0.138 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 137 LPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 137 lp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
.-.+..+|.+.+..+|++|....+|.+++.+
T Consensus 16 ~~~i~~~L~~a~~~vkr~L~~G~~P~eyQq~ 46 (68)
T PF08988_consen 16 ARAIEQQLRQAQSQVKRKLDRGGTPQEYQQL 46 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTCTSSHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 3467888999999999999999999987653
No 51
>TIGR02501 type_III_yscE type III secretion system protein, YseE family. Members of this family are found exclusively in type III secretion appparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis. This protein is small (about 70 amino acids) and not well characterized.
Probab=47.86 E-value=28 Score=23.28 Aligned_cols=30 Identities=23% Similarity=0.203 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCChhhhhc
Q psy12450 137 LPEILENLLSARKQAKNDLKKETDELTQVL 166 (168)
Q Consensus 137 lp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~ 166 (168)
.-.++..|.+.+..+|++|+...+|.+++.
T Consensus 15 ~~~~~~~L~~a~~~lk~qL~~~~tp~qYq~ 44 (67)
T TIGR02501 15 ARAIIEQLEAALAELKEQLSRGGDPQQYQE 44 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 678889999999999999999999998764
No 52
>PF07920 DUF1684: Protein of unknown function (DUF1684); InterPro: IPR012467 The sequences featured in this family are found in hypothetical archaeal and bacterial proteins of unknown function. The region in question is approximately 200 amino acids long. ; PDB: 2LOK_A 4DLH_A 2LNU_A.
Probab=34.70 E-value=66 Score=24.61 Aligned_cols=44 Identities=18% Similarity=0.353 Sum_probs=26.4
Q ss_pred cccceeeeeCCCCCCCcccCccEeecc-cCccccCCeEEeecCCcC
Q psy12450 44 TQKNFIIPTYHGGQGEDQFEGATVIEP-KKGYYADPIATLDFSSLY 88 (168)
Q Consensus 44 ~~~~~liP~~~~~~~~~~y~Gg~VleP-~~G~y~~pV~~lDF~SLY 88 (168)
...+..+|-.......+.|.||..|+- .++--.. -++|||+--|
T Consensus 68 ~~~~lfl~F~D~TsG~eTYg~gRyL~~~~~~~~~g-~v~lDFNrAy 112 (143)
T PF07920_consen 68 YGGGLFLPFRDATSGKETYGGGRYLDLPLPDDDAG-TVVLDFNRAY 112 (143)
T ss_dssp TCSSEEEEEEECCCCTTC-TT-EEEEE--TTTTTT-EEEEEGGGEB
T ss_pred CCCeEEEEEEeCCCCCcccCCceEEeccCCccCCC-eEEEECcCcc
Confidence 445667777754455677988755554 4554433 4799999766
No 53
>PRK15366 type III secretion system chaperone SsaE; Provisional
Probab=33.89 E-value=70 Score=22.18 Aligned_cols=29 Identities=28% Similarity=0.190 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHhccCCChhhhhc
Q psy12450 138 PEILENLLSARKQAKNDLKKETDELTQVL 166 (168)
Q Consensus 138 p~~L~~ll~~R~~~K~~mk~~~Dp~~k~~ 166 (168)
-.++..|=+.+...|+.|++..+|.+++-
T Consensus 19 ~~~i~~L~aa~~rL~~al~~P~sp~qYqq 47 (80)
T PRK15366 19 KGIILQLRAARKQLEENNGKLQDPQQYQQ 47 (80)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 67888999999999999999999998864
No 54
>COG0163 UbiX 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]
Probab=30.77 E-value=23 Score=28.57 Aligned_cols=65 Identities=20% Similarity=0.331 Sum_probs=38.8
Q ss_pred hhccC---cHHHHHHHHHH---HHHHHhccCCCccccccceeeeeCCCCCC----------CcccCccEeecccCccccC
Q psy12450 14 VRRDN---SPLVANMINTC---LQKLLINRDPDGAVTQKNFIIPTYHGGQG----------EDQFEGATVIEPKKGYYAD 77 (168)
Q Consensus 14 ~r~~~---c~Lv~~i~~~~---L~~lli~r~~~~A~~~~~~liP~~~~~~~----------~~~y~Gg~VleP~~G~y~~ 77 (168)
++.|. ||=+.+.+... +-.=|++|+-+=+++++.-++-... +.+ .-.-.||.|+.|.||||..
T Consensus 79 ~~~~gMiI~PCSmkTla~IA~G~~dnLi~RAAdV~LKErR~LVLv~R-EtPl~~ihLeNMlkl~~~GaiI~Pp~PaFY~~ 157 (191)
T COG0163 79 FRTDGMIIAPCSMKTLAAIAHGFADNLITRAADVALKERRPLVLVPR-ETPLSLIHLENMLKLAEMGAIIMPPMPAFYHK 157 (191)
T ss_pred CCcCcEEEEeCcHHHHHHHHhcccccHHHHHHHHHHhhCCceEEEec-cCCccHHHHHHHHHHHHCCCEecCCChhhhcC
Confidence 45555 55555555544 3344566665555555555555442 211 1234699999999999988
Q ss_pred Ce
Q psy12450 78 PI 79 (168)
Q Consensus 78 pV 79 (168)
|-
T Consensus 158 P~ 159 (191)
T COG0163 158 PQ 159 (191)
T ss_pred CC
Confidence 64
No 55
>KOG4498|consensus
Probab=24.33 E-value=79 Score=25.61 Aligned_cols=60 Identities=23% Similarity=0.289 Sum_probs=35.9
Q ss_pred hhhhccCcHHHHHHHHHH--HHHHHhccCCCccccccceeeeeCC-CC---CCCcccCccEeecccCcccc
Q psy12450 12 ETVRRDNSPLVANMINTC--LQKLLINRDPDGAVTQKNFIIPTYH-GG---QGEDQFEGATVIEPKKGYYA 76 (168)
Q Consensus 12 ~~~r~~~c~Lv~~i~~~~--L~~lli~r~~~~A~~~~~~liP~~~-~~---~~~~~y~Gg~VleP~~G~y~ 76 (168)
..|||..|-|++....-. +..++-+-.+.- =.+.|... .. -....|.|..+++|..++|.
T Consensus 56 ~~vRrpgCvlCR~~aadLa~l~~~ld~~Gv~L-----i~vg~g~~~~~~~f~~q~~f~gevylD~~~~~Y~ 121 (197)
T KOG4498|consen 56 AFVRRPGCVLCREEAADLASLKDLLDELGVVL-----IAVGPGSHVQFEDFWDQTYFSGEVYLDPHRGFYK 121 (197)
T ss_pred EEeccCcEEEeHHHHHHHHHHHHHHHHhCCEE-----EEEeccceeecchhhcccCcceeEEEcCccceec
Confidence 358999999998876655 566665443221 11222110 00 11234778899999999996
No 56
>PF15005 IZUMO: Izumo sperm-egg fusion
Probab=23.09 E-value=56 Score=25.58 Aligned_cols=29 Identities=28% Similarity=0.541 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHhccCCChhhhhccC
Q psy12450 140 ILENLLSARKQAKNDLKKETDELTQVLYC 168 (168)
Q Consensus 140 ~L~~ll~~R~~~K~~mk~~~Dp~~k~~l~ 168 (168)
+|++|+..|...|+.+++.--.++++.+|
T Consensus 91 ll~EL~~~r~~~~~~lk~~lk~fq~~a~c 119 (160)
T PF15005_consen 91 LLKELVWMRQNQKKELKKALKQFQKKACC 119 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 56689999999988888764456655444
No 57
>PF13854 Kelch_5: Kelch motif
Probab=22.39 E-value=67 Score=18.64 Aligned_cols=21 Identities=29% Similarity=0.398 Sum_probs=15.1
Q ss_pred ccEeecccCccccCCeEEeecCC
Q psy12450 64 GATVIEPKKGYYADPIATLDFSS 86 (168)
Q Consensus 64 Gg~VleP~~G~y~~pV~~lDF~S 86 (168)
||+.. .....+++ +.+||..|
T Consensus 21 GG~~~-~~~~~~~d-~~~l~l~s 41 (42)
T PF13854_consen 21 GGYSG-NNNSYSND-LYVLDLPS 41 (42)
T ss_pred cCccC-CCCCEECc-EEEEECCC
Confidence 67665 44556677 99999887
No 58
>PF13322 DUF4092: Domain of unknown function (DUF4092)
Probab=22.15 E-value=26 Score=27.64 Aligned_cols=14 Identities=36% Similarity=0.657 Sum_probs=10.5
Q ss_pred cCCcChhHHHhhcCCccc
Q psy12450 84 FSSLYPSIMMAHNLCYTT 101 (168)
Q Consensus 84 F~SLYPSIm~~~Ni~p~T 101 (168)
=+|+||||.. ||+.
T Consensus 152 GNs~Y~SIL~----CP~~ 165 (172)
T PF13322_consen 152 GNSMYNSILV----CPNN 165 (172)
T ss_pred cCCCCCceEE----CCCC
Confidence 4899999965 6654
No 59
>KOG3039|consensus
Probab=21.02 E-value=1.1e+02 Score=26.02 Aligned_cols=32 Identities=34% Similarity=0.469 Sum_probs=24.3
Q ss_pred eeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhcc
Q psy12450 118 YSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKK 157 (168)
Q Consensus 118 ~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~ 157 (168)
..++|.|+-|.+. .||+.+|.+.+++-++||.
T Consensus 56 Pvit~~GylfdrE--------aILe~ilaqKke~arrlka 87 (303)
T KOG3039|consen 56 PVITPDGYLFDRE--------AILEYILAQKKEIARRLKA 87 (303)
T ss_pred CccCCCCeeeeHH--------HHHHHHHHHHHHHHHHHHH
Confidence 4567899999873 6788888888887777763
Done!