Query gi|254781170|ref|YP_003065583.1| deoxyribodipyrimidine photolyase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 483
No_of_seqs 261 out of 3686
Neff 8.8
Searched_HMMs 39220
Date Mon May 30 06:16:15 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781170.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10674 deoxyribodipyrimidine 100.0 0 0 1121.3 36.7 471 7-481 1-472 (472)
2 TIGR03556 photolyase_8HDF deox 100.0 0 0 1059.0 33.7 460 8-476 1-470 (471)
3 COG0415 PhrB Deoxyribodipyrimi 100.0 0 0 1008.8 31.5 457 7-478 1-461 (461)
4 TIGR02765 crypto_DASH cryptoch 100.0 0 0 842.9 20.2 420 8-432 1-529 (529)
5 pfam03441 FAD_binding_7 FAD bi 100.0 0 0 726.4 15.4 268 210-478 1-275 (275)
6 KOG0133 consensus 100.0 0 0 658.1 19.1 467 9-482 6-498 (531)
7 TIGR02766 crypt_chrom_pln cryp 100.0 0 0 654.8 18.2 458 10-473 2-479 (481)
8 TIGR00591 phr2 deoxyribodipyri 100.0 0 0 374.6 13.3 397 8-428 23-471 (471)
9 pfam00875 DNA_photolyase DNA p 100.0 2.3E-40 5.6E-45 276.4 15.3 156 10-170 1-157 (164)
10 COG3046 Uncharacterized protei 99.9 9E-24 2.3E-28 170.9 17.0 402 9-430 3-451 (505)
11 pfam04244 DPRP Deoxyribodipyri 97.4 0.011 2.8E-07 36.8 13.1 140 21-168 11-157 (223)
12 KOG0133 consensus 92.0 0.0052 1.3E-07 38.8 -4.5 133 210-350 300-448 (531)
13 TIGR02963 xanthine_xdhA xanthi 81.9 0.84 2.2E-05 24.7 1.8 65 55-125 198-270 (515)
14 PRK00768 nadE NAD synthetase; 76.0 2.9 7.5E-05 21.3 3.1 49 395-445 157-211 (274)
15 pfam11940 DUF3458 Domain of un 74.9 2.3 5.9E-05 21.9 2.3 93 315-421 276-377 (408)
16 COG1087 GalE UDP-glucose 4-epi 71.2 3.3 8.4E-05 20.9 2.4 16 92-107 57-72 (329)
17 pfam04104 DNA_primase_lrg Euka 69.0 8.6 0.00022 18.3 5.0 63 330-397 97-167 (217)
18 TIGR01488 HAD-SF-IB HAD-superf 68.6 8.8 0.00022 18.2 4.2 70 37-110 61-138 (204)
19 cd01987 USP_OKCHK USP domain i 64.0 11 0.00027 17.7 7.8 71 31-111 24-94 (124)
20 pfam05268 GP38 Phage tail fibr 60.4 3.4 8.7E-05 20.8 0.8 13 57-69 19-31 (261)
21 cd00293 USP_Like Usp: Universa 60.1 13 0.00032 17.2 8.7 86 23-110 13-101 (130)
22 TIGR03333 salvage_mtnX 2-hydro 59.3 12 0.0003 17.4 3.4 15 252-266 8-22 (214)
23 COG3590 PepO Predicted metallo 59.3 3.1 7.9E-05 21.1 0.4 46 381-433 476-521 (654)
24 PRK09552 mtnX 2-hydroxy-3-keto 57.3 11 0.00029 17.5 3.0 82 252-336 11-93 (219)
25 pfam03392 OS-D Insect pheromon 56.6 4 0.0001 20.4 0.6 14 415-428 82-95 (95)
26 TIGR03531 selenium_SpcS O-phos 56.2 15 0.00037 16.8 6.9 81 65-146 191-281 (444)
27 PRK03980 flap endonuclease-1; 55.4 13 0.00034 17.1 3.1 37 88-131 82-118 (295)
28 PRK09568 DNA primase large sub 54.3 14 0.00037 16.9 3.1 47 337-385 216-262 (306)
29 cd01988 Na_H_Antiporter_C The 54.3 16 0.0004 16.6 9.8 85 24-109 14-101 (132)
30 pfam01902 ATP_bind_4 ATP-bindi 54.1 16 0.0004 16.6 6.1 94 23-128 14-108 (219)
31 TIGR01187 potA polyamine ABC t 50.6 15 0.00039 16.7 2.8 39 61-113 124-162 (331)
32 TIGR00338 serB phosphoserine p 48.8 19 0.00049 16.1 3.3 47 61-111 87-135 (223)
33 TIGR00273 TIGR00273 iron-sulfu 48.2 20 0.0005 16.0 5.6 68 64-137 52-120 (450)
34 pfam04045 P34-Arc Arp2/3 compl 46.8 8 0.0002 18.5 0.8 17 346-362 215-231 (242)
35 TIGR03674 fen_arch flap struct 46.4 21 0.00053 15.8 3.8 37 88-131 129-165 (338)
36 KOG2826 consensus 44.8 9.2 0.00023 18.1 0.9 17 346-362 260-276 (301)
37 TIGR01426 MGT glycosyltransfer 44.3 12 0.0003 17.4 1.4 42 388-440 288-331 (429)
38 TIGR01309 L30P_arch ribosomal 43.8 17 0.00044 16.4 2.2 53 243-296 46-102 (160)
39 COG2102 Predicted ATPases of P 41.5 25 0.00063 15.4 5.7 95 23-128 14-109 (223)
40 pfam10624 TraS Plasmid conjuga 40.9 10 0.00026 17.8 0.6 11 252-262 98-108 (164)
41 cd01994 Alpha_ANH_like_IV This 39.8 26 0.00067 15.2 6.7 94 24-128 14-111 (194)
42 PTZ00092 aconitate hydratase; 39.7 20 0.00052 15.9 2.0 10 418-427 634-643 (887)
43 TIGR00701 TIGR00701 conserved 36.5 26 0.00065 15.3 2.1 47 343-410 82-128 (151)
44 KOG3636 consensus 35.4 24 0.00061 15.5 1.8 34 350-383 398-437 (669)
45 TIGR00464 gltX_bact glutamyl-t 32.8 33 0.00084 14.6 2.2 29 337-372 274-302 (513)
46 PRK09613 thiH thiamine biosynt 31.9 24 0.00061 15.5 1.4 22 327-353 390-411 (471)
47 PRK10682 putrescine transporte 31.7 35 0.0009 14.4 3.9 78 370-476 289-368 (370)
48 COG1139 Uncharacterized conser 30.8 37 0.00094 14.3 6.2 70 61-136 63-133 (459)
49 TIGR03384 betaine_BetI transcr 29.9 38 0.00097 14.2 3.3 11 242-252 40-50 (189)
50 PRK11622 putative ABC transpor 29.9 31 0.00079 14.8 1.6 139 324-478 242-397 (401)
51 PTZ00217 flap endonuclease-1; 29.5 39 0.00098 14.2 4.0 85 36-131 80-173 (394)
52 TIGR03198 pucE xanthine dehydr 27.5 30 0.00077 14.8 1.2 25 319-343 120-149 (151)
53 PRK10490 sensor protein KdpD; 25.9 45 0.0011 13.7 10.8 97 22-128 262-362 (895)
54 TIGR02062 RNase_B exoribonucle 24.8 24 0.00061 15.5 0.3 19 338-356 471-492 (664)
55 TIGR01890 N-Ac-Glu-synth amino 24.4 34 0.00087 14.5 1.0 18 14-31 74-91 (439)
56 COG2217 ZntA Cation transport 24.3 48 0.0012 13.6 5.6 14 345-358 444-457 (713)
57 KOG0452 consensus 24.1 39 0.001 14.1 1.3 12 472-483 801-812 (892)
58 pfam05889 SLA_LP_auto_ag Solub 23.8 49 0.0012 13.5 9.8 120 10-147 103-232 (389)
59 PRK02249 DNA primase large sub 23.2 50 0.0013 13.4 3.8 64 334-399 223-286 (333)
60 pfam10406 TAF8_C Transcription 23.1 50 0.0013 13.4 3.3 42 423-476 1-42 (51)
61 TIGR00071 hisT_truA tRNA pseud 22.8 51 0.0013 13.4 1.7 22 342-363 272-293 (326)
62 pfam04858 TH1 TH1 protein. TH1 22.7 51 0.0013 13.4 2.4 22 241-262 286-307 (582)
63 COG4168 SapB ABC-type antimicr 22.4 34 0.00086 14.5 0.7 21 367-387 263-283 (321)
64 TIGR01316 gltA glutamate synth 22.3 52 0.0013 13.3 3.0 45 62-109 191-236 (462)
65 TIGR00750 lao LAO/AO transport 21.6 54 0.0014 13.2 2.1 13 341-353 268-280 (333)
66 COG5394 Uncharacterized protei 21.1 55 0.0014 13.2 2.7 35 329-365 69-104 (193)
67 TIGR00308 TRM1 N2,N2-dimethylg 21.0 56 0.0014 13.1 1.7 79 152-235 176-258 (462)
68 TIGR01621 RluA-like pseudourid 20.9 31 0.00079 14.8 0.3 15 94-108 32-46 (222)
69 pfam00440 TetR_N Bacterial reg 20.8 56 0.0014 13.1 2.4 24 335-358 1-24 (47)
70 COG1867 TRM1 N2,N2-dimethylgua 20.8 50 0.0013 13.5 1.3 32 315-348 317-348 (380)
71 cd04374 RhoGAP_Graf RhoGAP_Gra 20.5 57 0.0015 13.1 1.8 17 54-70 25-41 (203)
72 TIGR00597 rad10 DNA repair pro 20.4 34 0.00087 14.5 0.4 79 19-101 8-96 (117)
73 pfam08471 Ribonuc_red_2_N Clas 20.2 49 0.0013 13.5 1.2 36 252-287 41-81 (86)
No 1
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=100.00 E-value=0 Score=1121.27 Aligned_cols=471 Identities=55% Similarity=1.024 Sum_probs=429.9
Q ss_pred CCEEEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 64268883586755677899999995798299999738378478889989999999999999999997598099996575
Q gi|254781170|r 7 MSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSN 86 (483)
Q Consensus 7 M~~~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~ 86 (483)
|+++||||||||||+||+||.+|+++++++|+||||+||.+++.++.|.+|++|+++||.+|+++|+++|++|+++.++.
T Consensus 1 M~~~ivWFRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~i~~~~~ 80 (472)
T PRK10674 1 MTTHLVWFRNDLRLHDNLALAAACRDPSARVLALYIATPAQWAAHNMAPRQAAFINAQLNALQIALAEKGIPLLFHEVDD 80 (472)
T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf 97079996999756178999999977999699999985666406897999999999999999999997799779997676
Q ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 35089999999987097614210011100110010268887520000002234345557600237864432101479988
Q gi|254781170|r 87 FDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALI 166 (483)
Q Consensus 87 ~g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~~~~~~~~~~~~l~~p~~i~~~~~~~~~vftpf~k~~~ 166 (483)
+|+++++|.+++++++|+.||+|++|+++++.||..|++.++ ++.++.+++++|++|++|.++.+++|+|||||+++|.
T Consensus 81 ~~~~~~~l~~l~~~~~i~~v~~n~~~~~~~~~RD~~i~~~~~-~i~~~~~~~~~l~~p~~v~~~~~~~ykvfTpf~k~~~ 159 (472)
T PRK10674 81 FAASVEWVKQVCQQHQVTHLFYNYQYEVNERQRDVAVERTLR-NVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAFL 159 (472)
T ss_pred CCCHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHCC-CCEEEEECCCEEECCCCEECCCCCCCCCCCHHHHHHH
T ss_conf 546899999999980997899836457518999999998755-9828997581874655016799996764877889999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCC
Q ss_conf 631566322124554456776675557532347643-4554688876433322111111101101202686545666544
Q gi|254781170|r 167 QNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQ-AIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQL 245 (483)
Q Consensus 167 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tSrL 245 (483)
+......+..+|.|.........+..... .+.+.. .....++|||++|+++|++|+++++.+|.++||+|+.++||+|
T Consensus 160 ~~~~~~~p~~~p~p~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~gGE~~A~~~L~~Fl~~~~~~Y~~~Rn~P~~~~tSrL 238 (472)
T PRK10674 160 KRLREGDPECVPAPKVRSSGAIEPLPPIP-LNYPQQSFDTALFPVEEKAAIAQLRQFCQEGAGEYEQQRDFPAVEGTSRL 238 (472)
T ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 87321276558897644456789988533-37987776313579559999999999997247652411588676676656
Q ss_pred CHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHCCHHHHHH
Q ss_conf 61111464879999999999864311123477200102320246888788863357888615301101200010467899
Q gi|254781170|r 246 SPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQA 325 (483)
Q Consensus 246 SPyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~~~~~a 325 (483)
||||||||||||+||+++.+...+.. .+.+...|++||+|||||+|+++++|+++.++++.+.++.++|+.|++.|+|
T Consensus 239 SPyL~fG~IS~R~v~~~~~~~~~~~~--~~~~~~~~~~eL~WRef~~~~l~~~P~~~~~~~~~~~~~~~~w~~~~~~f~a 316 (472)
T PRK10674 239 SASLATGGLSPRQCLHRLLAEQPQAL--DGGAGSVWLNELIWREFYRHLMTAYPSLCKHRPFIAWTDRVQWQSNPAHLQA 316 (472)
T ss_pred CHHHHCCCCCHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCHHHHCCCCCCCHHHHHH
T ss_conf 89982963569999999999867520--2675288988889999999999978466542534155652776579899998
Q ss_pred HHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCCCCC
Q ss_conf 87227888688999999997167635899999999998410470022334776641331114745610020127898470
Q gi|254781170|r 326 WKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPY 405 (483)
Q Consensus 326 W~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~~~~ 405 (483)
||+|+|||||||||||||++||||||||||||||||||+|+||||+|++||+++|||||||||+|||||+||||+|++||
T Consensus 317 W~~G~TG~P~VDA~MR~L~~tGwm~nR~R~~vaSFl~~~L~idWr~g~~~f~~~l~D~d~~~n~~~Wqw~a~~G~d~~~~ 396 (472)
T PRK10674 317 WQQGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPY 396 (472)
T ss_pred HHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCC
T ss_conf 74799999627599999999769788999999999998649992778999999852257345873341112567888885
Q ss_pred CCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 2204645898872489978330082432799778049554013125789999763189999999999999996400
Q gi|254781170|r 406 FRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQS 481 (483)
Q Consensus 406 ~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~~~~~~~~~~YP~pivd~~~~~~~a~~~~~~~~k~~ 481 (483)
||||||++||++|||+|+|||||||||++||+++||+||+++...+++.|||+|||||++||++|+++|+++||.|
T Consensus 397 ~Ri~nP~~q~~~~Dp~g~fir~wvPEL~~~p~~~ih~Pw~~~~~~~~~~~YP~piVd~~~ar~~a~~~~~~~~k~~ 472 (472)
T PRK10674 397 FRIFNPTTQGERFDRDGEFIRRWLPELRDVPGKAIHEPWRWAEKAGVTLDYPQPIVDHKQARLATLAAYEAARKGA 472 (472)
T ss_pred CEEECHHHHHHHHCCCCCCHHHHCHHHHCCCHHHHCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf 2155787889985989876467386531699888349300764237678998565878999999999999986559
No 2
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=100.00 E-value=0 Score=1058.96 Aligned_cols=460 Identities=36% Similarity=0.658 Sum_probs=406.8
Q ss_pred CEEEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCC
Q ss_conf 42688835867556778999999957982999997383784788899899999999999999999975980999965753
Q gi|254781170|r 8 SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNF 87 (483)
Q Consensus 8 ~~~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~ 87 (483)
++.||||||||||+||+||.+|++.++ +|+||||+||.+++..+.|.+|++||++||.+|+++|+++|++|+|+.
T Consensus 1 ~~vlvWfRrDLRl~DN~aL~~A~~~~~-~vi~vyi~dp~~~~~~~~~~~r~~Fl~~sL~~L~~~L~~lg~~L~v~~---- 75 (471)
T TIGR03556 1 ALILFWHRRDLRLSDNIGLAAARQQSA-KVVGLFCLDPNILQADDMAPARVAYLIGCLQELQQRYQQAGSQLLILQ---- 75 (471)
T ss_pred CEEEEEECCCCCCCHHHHHHHHHHCCC-CEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEE----
T ss_conf 989999089975324799999995799-499999988256357998889999999999999999998799569998----
Q ss_pred CCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHH-HCCCCEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 50899999999870976142100111001100102688875-20000002234345557600237864432101479988
Q gi|254781170|r 88 DDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQ-HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALI 166 (483)
Q Consensus 88 g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~-~~~~~~~~~~~~l~~p~~i~~~~~~~~~vftpf~k~~~ 166 (483)
|+++++|++++++++|+.||+|++|++++..||+.|++.|+ .++.+..+++++|++|++|.++.+++|+|||||+|+|.
T Consensus 76 G~~~~vl~~l~~~~~i~~V~~n~~~~~~~~~RD~~v~~~l~~~gi~~~~~~~~~l~~p~~i~~~~~~~y~vftpf~k~~~ 155 (471)
T TIGR03556 76 GDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAVVTLWDQLLHSPDEILTGSGNPYTVYTPFWKNWS 155 (471)
T ss_pred CCHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCEEECCCCCCCCCCCHHHHHHH
T ss_conf 07899999999973987898616778489999999999998669734884653346867448999997664689999998
Q ss_pred HHCCCCCCCCCCCC-------CCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC
Q ss_conf 63156632212455-------44567766755575323476434-55468887643332211111110110120268654
Q gi|254781170|r 167 QNLVQADLRSLPVP-------AIRLTGPVTPSNIPRFFDYPFQA-IDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPA 238 (483)
Q Consensus 167 ~~~~~~~~~~~p~~-------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~ 238 (483)
+.....+.. .|.. ............+|...+.++.. ....++|||++|+++|++|+++++.+|+++||+|+
T Consensus 156 ~~~~~~p~~-~p~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~GE~~A~~~L~~Fl~~~~~~Y~~~Rn~P~ 234 (471)
T TIGR03556 156 SLPKPTPVA-TPTELEGLTEAELEAAAPLGVIALPTAKDLGFDWDGDLILEPGETAAQARLEEFCDRAIADYQEQRNFPA 234 (471)
T ss_pred HCCCCCCCC-CCHHCCCCCHHHHHHCCCCCCCCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 566678888-8310056884555213545544589978808775668878954999999999999856765223035867
Q ss_pred CCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHC-CCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHH
Q ss_conf 566654461111464879999999999864311-1234772001023202468887888633578886153011012000
Q gi|254781170|r 239 IQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLL-IKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWN 317 (483)
Q Consensus 239 ~~~tSrLSPyL~~G~IS~R~v~~~~~~~~~~~~-~~~~~~~~~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~ 317 (483)
.++||+|||||+|||||||+||+++++...... .....+..+|++||+|||||+|+++++|.+.. .++++.+++++|+
T Consensus 235 ~~~tSrLSPyL~fG~IS~R~v~~~~~~~~~~~~~~~~~~~~~~~~~eL~WRef~~~~l~~~P~~~~-~~~~~~~~~~~w~ 313 (471)
T TIGR03556 235 LDGTSQLSPALKFGVIGIRTVWQATQEAHENSRSEEARNSIRTWQQELAWREFYQHALYHFPELAD-GPYRSLFQNFPWE 313 (471)
T ss_pred CCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHC-CCCCCHHCCCCCC
T ss_conf 668887788881787779999999999987322544333589999999988999999985837442-7664111036776
Q ss_pred CCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEE
Q ss_conf 10467899872278886889999999971676358999999999984104700223347766413311147456100201
Q gi|254781170|r 318 KDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAAS 397 (483)
Q Consensus 318 ~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~ 397 (483)
+|++.|+|||+|+|||||||||||||++||||||||||||||||||+|+||||+||+||+++|||||||||+|||||+||
T Consensus 314 ~~~~~~~aW~~G~TG~P~VDA~MR~L~~TGwmhnR~R~~vaSFl~~~L~idWr~G~~~f~~~liD~D~a~n~~~Wqw~a~ 393 (471)
T TIGR03556 314 NNEAHFQAWCEGRTGYPIVDAAMRQLNETGWMHNRCRMIVASFLTKDLIINWQWGEKYFMQKLIDGDLAANNGGWQWSAS 393 (471)
T ss_pred CCHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHCHHCCCEEEC
T ss_conf 88799702378999998363899999975896889999999999860599837899999986425662114122622214
Q ss_pred CCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 2789847022046458988724899783300824327997780495540131257899997631899999999999999
Q gi|254781170|r 398 TGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYA 476 (483)
Q Consensus 398 ~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~~~~~~~~~~YP~pivd~~~~~~~a~~~~~~ 476 (483)
||+|++| ||||||++||++|||+|+|||||||||++||+++||+||..+.. ....|||.|||||++||++|+++|++
T Consensus 394 ~G~d~~~-~Rifnp~~q~~~~Dp~g~fir~wvPEL~~~p~~~i~~~~~~~~~-~~~~~YP~PiVd~~~~r~~a~~~~~~ 470 (471)
T TIGR03556 394 SGMDPKP-LRIFNPASQAQKFDPEAEYIRRWLPELRSVDTKDLVTGKITPLE-RRAVGYPLPIVDHNQQQQLFKQLYQQ 470 (471)
T ss_pred CCCCCCC-CEEECHHHHHHHHCCCCCEEHHHCHHHCCCCHHHHCCCCCCCHH-HCCCCCCCCCCCHHHHHHHHHHHHCC
T ss_conf 6789997-72108889899859898870462886327998883697679033-30269983338789999999999732
No 3
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=1008.76 Aligned_cols=457 Identities=48% Similarity=0.806 Sum_probs=412.3
Q ss_pred CCEEEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCC
Q ss_conf 64268883586755677899999995798299999738378478889989999999999999999997598099996575
Q gi|254781170|r 7 MSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSN 86 (483)
Q Consensus 7 M~~~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~ 86 (483)
|+++|||||||||++||+||.+|++.+...+++|||++|.++. ++|++|.+|+.+||.+|+++|+++|++|++..
T Consensus 1 ~~~~l~WfrrDLR~~DN~aL~~A~~~~~~~~~~vfi~~~~~~~--~~~~~~~~Fl~~sL~~L~~~L~~~gi~L~v~~--- 75 (461)
T COG0415 1 TSTVLVWFRRDLRLTDNAALAAACQSGQPVIIAVFILDPEQLG--HASPRHAAFLLQSLQALQQSLAELGIPLLVRE--- 75 (461)
T ss_pred CCEEEEEECCCCCCCCHHHHHHHHHCCCCCEEEEEEECHHHCC--CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEE---
T ss_conf 9707999406554677599999985378735899985500100--03799999999999999999997499459982---
Q ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHH-HCCCCEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 350899999999870976142100111001100102688875-2000000223434555760023786443210147998
Q gi|254781170|r 87 FDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQ-HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKAL 165 (483)
Q Consensus 87 ~g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~-~~~~~~~~~~~~l~~p~~i~~~~~~~~~vftpf~k~~ 165 (483)
|++.+++++++++.+++.||+|++|++++..||.+|...|. .++.+++++++++++|+++.++.+++|+|||||+|+|
T Consensus 76 -~~~~~~l~~~~~~~~~~~v~~n~~~~~~~~~rD~al~~~l~~~gi~~~~~~d~~l~~p~~~~t~~~~~y~vfT~F~k~~ 154 (461)
T COG0415 76 -GDPEQVLPELAKQLAATTVFWNRDYEEWERQRDAALAQPLTEVGIAVHSFWDALLHEPGEVRTGSGEPYKVFTPFYKAW 154 (461)
T ss_pred -CCHHHHHHHHHHHHCCCEEEEEEEECHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHCCCCCCCCCCCCCHHHHHH
T ss_conf -8879999999998185068850010563888999999888763954788545201577661379999765266699988
Q ss_pred HHHCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC
Q ss_conf 86315663221245544567-766755575323476--434554688876433322111111101101202686545666
Q gi|254781170|r 166 IQNLVQADLRSLPVPAIRLT-GPVTPSNIPRFFDYP--FQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGT 242 (483)
Q Consensus 166 ~~~~~~~~~~~~p~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~t 242 (483)
...... ..+.+.|..... ....+ .+.....+ .......|.|||++|+++|++|+.+++.+|.+.||+|+.++|
T Consensus 155 ~~~~~~--~~~~~~p~~~~~~~~~~~--~~~~~~~P~~~~~~~~~~~~Ge~aA~~~l~~F~~~~l~~Y~~~Rd~p~~~~T 230 (461)
T COG0415 155 RDRLRI--LRPVPAPDVLDALRDEEP--PPEEISLPDFSKFDVLLFTGGEKAALARLQDFLAEGLDDYERTRDFPALDGT 230 (461)
T ss_pred HHHCCC--CCCCCCCCHHCCCCCCCC--CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 875135--788899512103343446--7520018862224455789358999999999999888788874577564665
Q ss_pred CCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHCCHHH
Q ss_conf 54461111464879999999999864311123477200102320246888788863357888615301101200010467
Q gi|254781170|r 243 SQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHL 322 (483)
Q Consensus 243 SrLSPyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~~~ 322 (483)
|+|||||+||+||||+||++++++... .++++..|++||+|||||+|++.++|+++...++...++.++|.++++.
T Consensus 231 S~LSpyL~~G~IS~r~v~~~~~~~~~~----~~~~~~~~~~eL~WREFy~h~~~~~p~~~~~~~~~~~~~~~~w~~~~~~ 306 (461)
T COG0415 231 SRLSPYLAFGVISPREVYAALLAAESD----AREGTAALINELIWREFYQHLLYHYPSLSRFEPFAEKTLNIPWEDNPAH 306 (461)
T ss_pred CCCCHHHHCCCCCHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf 666889982886899999999976503----6401899999999999999999838853235641102457861269999
Q ss_pred HHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCC
Q ss_conf 89987227888688999999997167635899999999998410470022334776641331114745610020127898
Q gi|254781170|r 323 LQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDS 402 (483)
Q Consensus 323 ~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~ 402 (483)
|++||+|+|||||||||||||++||||||||||+|||||||+|.||||+||+||+++|||||+|+|+|||||+||||+|+
T Consensus 307 f~aW~~G~TGyPIVDA~MRqL~~TG~MHNR~RMivAsFL~k~L~IdWR~GE~~F~~~LiD~D~asN~ggWQW~AstG~Da 386 (461)
T COG0415 307 FQAWQEGKTGYPIVDAAMRQLNQTGYMHNRMRMIVASFLTKDLLIDWREGEKYFMRQLIDGDPASNNGGWQWAASTGTDA 386 (461)
T ss_pred HHHHHCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCC
T ss_conf 99986589899533389999998678412789999999998238877778999998544777556777735773168888
Q ss_pred CCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 4702204645898872489978330082432799778049554013125789999763189999999999999996
Q gi|254781170|r 403 VPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAK 478 (483)
Q Consensus 403 ~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~~~~~~~~~~YP~pivd~~~~~~~a~~~~~~~~ 478 (483)
+||||||||++|++||||+|+|||+|||||++||+++||+||+++. ..++.+||.|||||+++|++|+++|+.+|
T Consensus 387 ~pyfRiFNp~~Q~~kfDp~g~fIr~wvPeL~~~~~~~ih~p~~~~~-~~~~~~YP~piVd~~~~r~~a~~~y~~~~ 461 (461)
T COG0415 387 APYFRIFNPVTQAEKFDPDGEFIRRWVPELRNLPDKYIHEPWELSE-VVLGVDYPKPIVDHKESREQALAAYEAAK 461 (461)
T ss_pred CCCEECCCHHHHHHHCCCCCCCHHHHCHHHHCCCHHHCCCHHHCCC-CCCCCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 8630003878887652888532886488864798553148654433-11257898210154788999999987229
No 4
>TIGR02765 crypto_DASH cryptochrome, DASH family; InterPro: IPR014133 Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This entry describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes..
Probab=100.00 E-value=0 Score=842.89 Aligned_cols=420 Identities=29% Similarity=0.509 Sum_probs=357.4
Q ss_pred CEEEEEECCCCCCCCCHHHHHHHHHCC----CCEEEEEEECHHHHCC----------------C------CCCHHHHHHH
Q ss_conf 426888358675567789999999579----8299999738378478----------------8------8998999999
Q gi|254781170|r 8 SVHLVWLRNDLRITDNKALYAACHNSD----AKVIAVFIATPEQWRQ----------------H------GISARQSHFI 61 (483)
Q Consensus 8 ~~~IvWfRrDLRl~DN~aL~~A~~~~~----~~vlpvyi~dp~~~~~----------------~------~~~~~~~~Fl 61 (483)
.+.|+|||+||||+||++|+.|.+.++ ..|||||||||.+... . ..|+.|.+||
T Consensus 1 k~vl~wfRnDLRl~DN~~l~~A~~~~~~~~~~~l~p~YCfd~~~~~l~GfvPkGsenPhPaPk~~~~~~~~~G~~R~~FL 80 (529)
T TIGR02765 1 KVVLYWFRNDLRLHDNELLHKASSKADKSSFSELVPLYCFDPRQFKLSGFVPKGSENPHPAPKTHFGGFPKTGPFRAKFL 80 (529)
T ss_pred CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 96899971422203027999997314331750589885047655554111237777788886555576000115666789
Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCC-----CCCEEEEC-CCCCHHHHCCHHHHHHHHH-CCC--
Q ss_conf 99999999999975980999965753508999999998709-----76142100-1110011001026888752-000--
Q gi|254781170|r 62 YASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQR-----VTKLFYNR-QYEINEVRRDKLLEKRLQH-RVI-- 132 (483)
Q Consensus 62 ~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~-----i~~v~~n~-~~~~~~~~rd~~i~~~l~~-~~~-- 132 (483)
.|||.||+.+|+++|+.|.|+. |.+.++|.+|+++.+ |++||++. +.+.+|...+..|++.|.. .+.
T Consensus 81 ~esv~DL~~~L~~~G~~LlVr~----G~p~~vl~~L~~~~~~keCqv~~v~~~~t~~gSeE~~~~~~l~~~~~~~~~~S~ 156 (529)
T TIGR02765 81 LESVADLRTSLRKLGSDLLVRA----GKPEDVLPELIKELEAKECQVRAVFLHQTEVGSEEKSVERKLQQALAKLGIHSA 156 (529)
T ss_pred HHHHHHHHHHHHHHCHHHCCCC----CCHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCE
T ss_conf 9999999999987150220048----887899999998631133301234422631203689999999987432377520
Q ss_pred -CEECCCCC--CCCCCCCCCC----CCCCCCCCHHHHHHHHH-HCCCCCCCCC-------CCCCCCCCCCCCCCC-CC--
Q ss_conf -00022343--4555760023----78644321014799886-3156632212-------455445677667555-75--
Q gi|254781170|r 133 -CKSFDDSV--LLPPGSILNH----ALQMYKVYTPFRKALIQ-NLVQADLRSL-------PVPAIRLTGPVTPSN-IP-- 194 (483)
Q Consensus 133 -~~~~~~~~--l~~p~~i~~~----~~~~~~vftpf~k~~~~-~~~~~~~~~~-------p~~~~~~~~~~~~~~-~~-- 194 (483)
+..+++++ |++..+++.. ....|.|||+|||+++. .....++... |.|.+.......+.. +|
T Consensus 157 ~~~~~w~~tkyL~h~~dLPF~~tsGl~dLPdvFTqFRK~VE~l~~~~~~~~~~P~~~~Lp~~P~~dmi~~~~~g~~~PGf 236 (529)
T TIGR02765 157 KVEQFWGSTKYLYHEDDLPFDHTSGLEDLPDVFTQFRKQVEALKISIRPPLPAPEKGELPPLPKIDMISVEDPGWQIPGF 236 (529)
T ss_pred EEEECCCCCCEECCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 35654587101103355783011243446522130101001000011366788856677778743311367788888873
Q ss_pred CCCCCCCCCCC------------------CCCCCCCCCCCCCCCCCCC-CC-CCHHHHCCC-CCCCCCCCCCCHHHCCCC
Q ss_conf 32347643455------------------4688876433322111111-10-110120268-654566654461111464
Q gi|254781170|r 195 RFFDYPFQAID------------------PMFPIGEQNALHILRKFCK-EK-VYYYVEQRD-IPAIQGTSQLSPYLSIGV 253 (483)
Q Consensus 195 ~~~~~~~~~~~------------------~~~~gGe~~A~~~L~~Fl~-~~-l~~Y~~~Rn-~p~~~~tSrLSPyL~~G~ 253 (483)
++.+++..... -.|.|||++|++++++++. .. ++.|+++|| ..+.|.+|+||||||+||
T Consensus 237 ~~~~L~~~~~~~~~~~~~~~~~~~~~~S~~~F~GGE~~aL~r~~~Yf~~~~~~~~YKeTRNGllG~DySTKFSPWLAlGC 316 (529)
T TIGR02765 237 TLEDLGEEESEIVKFLKDLIDFPEDERSVLDFKGGETSALARLKEYFWSKDLLKSYKETRNGLLGPDYSTKFSPWLALGC 316 (529)
T ss_pred CHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCCCHHHHHHHHHHHCC
T ss_conf 13530565147899976303662001332026675357889999874146665342111000146541146789987246
Q ss_pred CCHHHHHHHHHHHHH----------HHCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHCCHH--
Q ss_conf 879999999999864----------31112347720010232024688878886335788861530110120001046--
Q gi|254781170|r 254 LSPRQCWNRLKEEFV----------DLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSH-- 321 (483)
Q Consensus 254 IS~R~v~~~~~~~~~----------~~~~~~~~~~~~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~~-- 321 (483)
||||+|+.++++++. .-....|+|+++.+.||+|||||+++...|++.+|.-+... ....+|..|.+
T Consensus 317 vSpR~I~~~l~~YE~GtGtkykGadGf~~~~N~STYWv~FELLWRdYF~f~A~KyG~rLF~~~G~~-g~~~~w~~d~~ky 395 (529)
T TIGR02765 317 VSPRQIYEELQRYETGTGTKYKGADGFERGANDSTYWVIFELLWRDYFRFYALKYGNRLFRFSGLR-GKHPKWSFDAKKY 395 (529)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCEEECCCCC-CCCCCCCHHHHHH
T ss_conf 688899999997522377421046664441365203457788889999999998386012046767-7888750046550
Q ss_pred -----------------------HHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf -----------------------789987227888688999999997167635899999999998410470022334776
Q gi|254781170|r 322 -----------------------LLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMS 378 (483)
Q Consensus 322 -----------------------~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~ 378 (483)
.|++|++|+|||||||||||||.+||||+||+||+|||||||+|+||||.||+||+.
T Consensus 396 GWrtantsialPGqePtPekvse~F~~Wk~G~TGyPlvdAnMreL~~TGfMSNRGRQ~VASfLv~~LGlDWRyGAewFE~ 475 (529)
T TIGR02765 396 GWRTANTSIALPGQEPTPEKVSERFEAWKTGTTGYPLVDANMRELAATGFMSNRGRQNVASFLVKDLGLDWRYGAEWFET 475 (529)
T ss_pred CCCCCCCEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf 44100221445888887468999999860787578730222785621267334057899999987357654221788851
Q ss_pred HHHCCCHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHH
Q ss_conf 641331114745610020127898470220464589887248997833008243
Q gi|254781170|r 379 QLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPEL 432 (483)
Q Consensus 379 ~llD~d~~~n~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL 432 (483)
+|||||++||||||||.||+|+||+...|+||++||+++|||+|+||++|||||
T Consensus 476 ~L~DYDV~SNWGNW~Y~AGVGnDPRga~R~FN~~KQa~~YDp~Geyv~~W~~~l 529 (529)
T TIGR02765 476 QLVDYDVSSNWGNWQYLAGVGNDPRGANRQFNLEKQAQDYDPDGEYVKTWVPEL 529 (529)
T ss_pred HHHHCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCHHHHCCCCC
T ss_conf 211036552425655105788875534666573543025687863786406779
No 5
>pfam03441 FAD_binding_7 FAD binding domain of DNA photolyase.
Probab=100.00 E-value=0 Score=726.41 Aligned_cols=268 Identities=51% Similarity=0.921 Sum_probs=252.8
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCHHH
Q ss_conf 87643332211111110110120268654566654461111464879999999999864311123477200102320246
Q gi|254781170|r 210 IGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWRE 289 (483)
Q Consensus 210 gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tSrLSPyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~eL~WRe 289 (483)
|||++|+++|++|+++++.+|.++||.|+.++||+|||||+|||||+|+|++++.+...........++++|++||+|||
T Consensus 1 GGe~~A~~~L~~Fl~~~l~~Y~~~Rn~P~~~~tS~LSpyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~f~~eL~WRe 80 (275)
T pfam03441 1 GGEKAALKRLESFLKERLADYAKDRDDPAADGTSRLSPYLHFGEISPRQVYQAVRKAAGAPGSAASEGAEAFLSELIWRE 80 (275)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 94999999999999868877534038888767764679880896869999999999873103544211999999999999
Q ss_pred HHHHHHHHHHHHHHHHHCCHHHHCCCHHCCH---HHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC
Q ss_conf 8887888633578886153011012000104---6789987227888688999999997167635899999999998410
Q gi|254781170|r 290 FYRHLMAFYPSVCMGKPFIPWTEKIEWNKDS---HLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLL 366 (483)
Q Consensus 290 f~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~---~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~ 366 (483)
||+++++++|++.. .++++.++.++|..++ +.|++|++|+||||+||||||||++||||||||||||||||||+|+
T Consensus 81 f~~~~~~~~p~~~~-~~~~~~~~~~~w~~~~~~~~~~~aW~~G~TG~P~vDA~mrqL~~tG~mhnr~Rm~vAsfl~k~L~ 159 (275)
T pfam03441 81 FYIQLLYHNPDLER-ENLNPAYDGLPWAKDRPDEYLLEAWEEGRTGYPLVDAAMRQLRQTGWMHNRLRMIVASFLTKKLL 159 (275)
T ss_pred HHHHHHHHCCCHHH-HCCCHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCC
T ss_conf 99999985862765-32678773687556743299999987599899619999999999889668999999999998736
Q ss_pred CCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHH
Q ss_conf 47002233477664133111474561002012789847022046458988724899783300824327997780495540
Q gi|254781170|r 367 VDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSW 446 (483)
Q Consensus 367 idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~ 446 (483)
||||.|++||+++|||||||||++||||+||||+|++||||||||++|+++|||+|+|||+|||||++||+++||+||++
T Consensus 160 idWr~G~~~f~~~LiD~D~a~N~~~Wqw~agtg~d~~p~~Ri~np~~q~~~~Dp~g~yir~wvPeL~~~p~~~ih~Pw~~ 239 (275)
T pfam03441 160 IDWREGEEYFAETLIDADPASNNGGWQWQAGTGTDAAPYFRIFNPVKQSDKFDPNGEYIRRWVPELAGLPDRYIHEPWKA 239 (275)
T ss_pred CCHHHHHHHHHHHCCCCCHHHCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHCHHHHCCCHHHHCCCCCC
T ss_conf 88689999999876564653477877888477888875433569988999859896559997877526998884795438
Q ss_pred HHH----CCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 131----25789999763189999999999999996
Q gi|254781170|r 447 LDK----NDLSLNYPLPIVDHKKACHHTLNQYYAAK 478 (483)
Q Consensus 447 ~~~----~~~~~~YP~pivd~~~~~~~a~~~~~~~~ 478 (483)
+.. ..+|.+||+||||++++|++|+++|+++|
T Consensus 240 ~~~~~~~~~~~~~YP~Pivd~~~~r~~~~~~~~~~~ 275 (275)
T pfam03441 240 PRPVQAGAVLGKDYPKPIVDHKEARKRALDAYKAAR 275 (275)
T ss_pred CHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHC
T ss_conf 878887612479997133888999999999999719
No 6
>KOG0133 consensus
Probab=100.00 E-value=0 Score=658.14 Aligned_cols=467 Identities=30% Similarity=0.434 Sum_probs=389.0
Q ss_pred EEEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC
Q ss_conf 26888358675567789999999579829999973837847888998999999999999999999759809999657535
Q gi|254781170|r 9 VHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFD 88 (483)
Q Consensus 9 ~~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g 88 (483)
.+|+|||+||||||||||.+|+..++ +|.||||+||+..+....|..+++|+.|||.+|+++|+++|++|.+++ +
T Consensus 6 ~~v~wfr~~lR~~dnpal~~a~~~~~-~~~~v~i~d~~~~~~~~~g~~~~~~l~qsL~~ld~sl~~l~~~L~v~~----~ 80 (531)
T KOG0133 6 KSVHWFRKGLRLHDNPALLAAAAGKE-PVRPVFILDPEEAGSSNVGRNRWRFLLQSLEDLDQSLRELNSRLFVFR----G 80 (531)
T ss_pred CEEEECCCCCCCCCCHHHHHHHCCCC-CCEEEEEECHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEE----C
T ss_conf 35775204853135733688755578-730179758767413465556799999988888999998579668984----7
Q ss_pred CHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHH-CCCCEECCCCCCCCCCCCCC-CCCCCCCCCHHHHHHHH
Q ss_conf 08999999998709761421001110011001026888752-00000022343455576002-37864432101479988
Q gi|254781170|r 89 DSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH-RVICKSFDDSVLLPPGSILN-HALQMYKVYTPFRKALI 166 (483)
Q Consensus 89 ~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~-~~~~~~~~~~~l~~p~~i~~-~~~~~~~vftpf~k~~~ 166 (483)
.++.+|+++.+..+++.|.++.+++|....||..++..+.+ ++.+.+...++++.|+.+.. +.++++-.+.+|+....
T Consensus 81 ~p~~vl~~~~~~~~~~~l~~~~~~~p~~~vrD~~~~~~a~~l~i~v~s~~s~~~~~~~~~i~~n~~k~pls~~~~~~~~~ 160 (531)
T KOG0133 81 HPIAVLSRLLEQVGVQKLKFEYDMEPDGKVRDATIKSLATELGLSVVSPVSHTLYLPDKIIEANGGKPPLSYKTFRGVCQ 160 (531)
T ss_pred CCHHHHHHHHHCCCEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHCHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 71688765220134069989985268650102899999998524222667235446899998417888600023102032
Q ss_pred HHCCCCCC----CCCCCCCC-C-CCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCC--CHHHHCCC
Q ss_conf 63156632----21245544-5-6776675557532347643---4554688876433322111111101--10120268
Q gi|254781170|r 167 QNLVQADL----RSLPVPAI-R-LTGPVTPSNIPRFFDYPFQ---AIDPMFPIGEQNALHILRKFCKEKV--YYYVEQRD 235 (483)
Q Consensus 167 ~~~~~~~~----~~~p~~~~-~-~~~~~~~~~~~~~~~~~~~---~~~~~~~gGe~~A~~~L~~Fl~~~l--~~Y~~~Rn 235 (483)
+......+ .....+.. . .........++.+..+.+. .....|+||++.|+.+|+.|+...+ .++....+
T Consensus 161 ~~~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~v~~~e~l~~~~~~~~~~~~~~g~s~al~~l~~~l~~~~~~an~~~~~~ 240 (531)
T KOG0133 161 SMSAPKIPALVLSGLAVEKHPNFLANSKASAVVPTLELLRFIPSNYGEVVWRGGESEALKRLDAHLKVPLWVANLELRYS 240 (531)
T ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 23645554323556657777056652245535677032145732123112577532025899987547887764305456
Q ss_pred CC-C--CCCCCCCCHHHCCCCCCHHHHHH--HHHHHHHHHCCCCCCCCHH-HCCCCCHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf 65-4--56665446111146487999999--9999864311123477200-10232024688878886335788861530
Q gi|254781170|r 236 IP-A--IQGTSQLSPYLSIGVLSPRQCWN--RLKEEFVDLLIKPKSGAFS-WLNELIWREFYRHLMAFYPSVCMGKPFIP 309 (483)
Q Consensus 236 ~p-~--~~~tSrLSPyL~~G~IS~R~v~~--~~~~~~~~~~~~~~~~~~~-fl~eL~WRef~~~~~~~~P~~~~~~~~~~ 309 (483)
.+ + ..+++.|||||+|||+|+|.+++ .+.+.. ....+.+.+.++ |+.|+.|||||++.....|.. ....++.
T Consensus 241 ~~~~~~~~s~~~Ls~yL~fg~~svr~~~~~~~~k~V~-~~~~~~s~~~es~~~~qv~Wre~~y~~~~n~p~~-~~m~~n~ 318 (531)
T KOG0133 241 NANSRVKISTTVLSPYLKFGCLSVRYFYRCVRLKQVK-WKAKKNSLPPESLFLGQVAWREFFYTAAFNTPYF-DDMPGNK 318 (531)
T ss_pred CCCHHCCCCCCCCCCCEEECCCEEEEEHHHHHHHHHH-HHHHCCCCCCCCCCCCEEEEECHHHHHHCCCCCC-CCCCCCC
T ss_conf 6210047872215613265243167404576799999-8653036776444332255312456751278542-4564554
Q ss_pred HHHCCCHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHCCCHHCC
Q ss_conf 110120001046789987227888688999999997167635899999999998-4104700223347766413311147
Q gi|254781170|r 310 WTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVK-DLLVDWRIGEEYFMSQLLDGDLASN 388 (483)
Q Consensus 310 ~~~~~~w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~-~L~idWr~g~~~f~~~llD~d~~~n 388 (483)
.+.+++|..|+..|++|.+|+||||+|||+||||.+|||||+|.|++||||+|+ +|+|+||+|.++|+++|+|+|.++|
T Consensus 319 ~~~~ipw~~n~~~~~aw~~G~tG~P~ida~m~~l~~~gw~h~~~R~~vasf~tr~~L~i~w~eg~~~F~~~llD~D~~~~ 398 (531)
T KOG0133 319 ILLQIPWDKNPPKLAAWLEGLTGYPWLDAGMRQLLASGWEHHRSRTIVASFLTRGDLLISWREGLDVFMEYLLDADSSKN 398 (531)
T ss_pred CCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCEEEEHHHHHHHHHHHHCCHHHHCC
T ss_conf 21238755571555788707889973459999999988875323113576740351132389899999987336043238
Q ss_pred CCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHHHH------HCCCCCCCCCCCCC
Q ss_conf 456100201278984702204645898872489978330082432799778049554013------12578999976318
Q gi|254781170|r 389 NGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLD------KNDLSLNYPLPIVD 462 (483)
Q Consensus 389 ~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~~~------~~~~~~~YP~pivd 462 (483)
.|||+|++|++.+..+++|||||+.|++++||+|.|||+|+|||++.|.++||+||..+. .+.+|.|||+|||+
T Consensus 399 agnW~~~S~~s~f~~~~~~~ysp~~~~kk~dP~g~yir~~lp~l~~~p~~~i~~pW~~p~~~~~~~~~~lg~~Yp~~iv~ 478 (531)
T KOG0133 399 AGNWMWLSSTSHFFDQFDRVYSPVALGKKLDPDGLYIRQWLPELRSGPMHFIYEPWAAPEGVQTAAGELLGVDYPKPIVK 478 (531)
T ss_pred CCCCCEECCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHHHCCCCHHHHH
T ss_conf 77654122664001466613389998276796412588871998618861001688885777643003430145333421
Q ss_pred HHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999999999999964007
Q gi|254781170|r 463 HKKACHHTLNQYYAAKKQSL 482 (483)
Q Consensus 463 ~~~~~~~a~~~~~~~~k~~~ 482 (483)
+..++++..+++.++.....
T Consensus 479 ~~~a~k~~~e~~~~~~~~~~ 498 (531)
T KOG0133 479 LASAAKRNMEAMGCMWSIGA 498 (531)
T ss_pred HHHHHHHHHHHHHHHHHHCC
T ss_conf 67766768888888875015
No 7
>TIGR02766 crypt_chrom_pln cryptochrome, plant family; InterPro: IPR014134 At least five major families of cryptochromes and photolyases share FAD cofactor binding, sequence homologues, and the ability to react to short wavelengths of visible light. Photolyases are responsible for light-dependent DNA repair by removal of two types of UV-induced DNA dimerisation. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light..
Probab=100.00 E-value=0 Score=654.82 Aligned_cols=458 Identities=29% Similarity=0.521 Sum_probs=398.1
Q ss_pred EEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCC
Q ss_conf 68883586755677899999995798299999738378478889989999999999999999997598099996575350
Q gi|254781170|r 10 HLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDD 89 (483)
Q Consensus 10 ~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g~ 89 (483)
+|||||||||+.|||||.+|++. +.|+|+||+.|...+....|....+|+.+||..|+++|+.+|..|+..+. .+
T Consensus 2 ~~vWfrrdlr~~dnPala~a~~~--G~v~~~f~W~P~~~G~~~PGr~srWWl~~sl~~l~~sl~~lG~~l~~~~~---~~ 76 (481)
T TIGR02766 2 TVVWFRRDLRVEDNPALAAAARE--GEVLPVFVWAPEEEGQFYPGRVSRWWLKQSLAHLSQSLRSLGAKLVLIRS---ED 76 (481)
T ss_pred EEEEEECCCCCCCCHHHHHHHHC--CCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HH
T ss_conf 06876400220366478887525--97489998634457861786204788999999999999862058778854---88
Q ss_pred HHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHH-HCCCCEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 899999999870976142100111001100102688875-2000000223434555760023786443210147998863
Q gi|254781170|r 90 SIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQ-HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQN 168 (483)
Q Consensus 90 ~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~-~~~~~~~~~~~~l~~p~~i~~~~~~~~~vftpf~k~~~~~ 168 (483)
.+..|.++++..++++|++|+-|+|-...||.++++.+. .++.+.+|++.+|++|++|....|++++.|..||++|++.
T Consensus 77 ~~~~ll~~~~~~Ga~~~~fnhlydP~slvrd~~~k~~l~~~Gi~~~sfn~dllyePWe~~~~~G~~f~~f~~~W~~Cl~~ 156 (481)
T TIGR02766 77 TVEALLDVVRSTGATRLVFNHLYDPVSLVRDHRVKEKLAAEGISVQSFNADLLYEPWEVYDEKGKAFTMFAAYWEKCLEL 156 (481)
T ss_pred HHHHHHHHHHHCCCCEEHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCEEECCCCCHHHHHHHHHHHHCC
T ss_conf 99999999975064001033312623332226899999857845776153101275001205786135788999986147
Q ss_pred CCCCCCCCCCCCCCC---CCCCCCCCCCCCCC--C---CCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
Q ss_conf 156632212455445---67766755575323--4---764-34554688876433322111111101101202686545
Q gi|254781170|r 169 LVQADLRSLPVPAIR---LTGPVTPSNIPRFF--D---YPF-QAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAI 239 (483)
Q Consensus 169 ~~~~~~~~~p~~~~~---~~~~~~~~~~~~~~--~---~~~-~~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~ 239 (483)
.........+...+. ....+..+.+..+. + .+. ..+...|-+|-..|.+.|+.|++..+-.|.+.+.....
T Consensus 157 ~~~~~~~~~~P~~~~p~~~~~~~~~C~~~~l~~e~~~e~~snall~raWsPGW~n~~k~l~~f~~~~l~~y~~~~~k~~~ 236 (481)
T TIGR02766 157 PIDAESPLLPPKKLVPVTASEDVSACSVDDLVLEDDSEKGSNALLARAWSPGWSNADKLLEEFINKPLLEYSKNRKKVDG 236 (481)
T ss_pred CCCCCCCCCCCCCEEECCCHHHHHHCCCHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 54520024785203312321234430100100233223202456443237771127899999863367877653000000
Q ss_pred CCCCCCCHHHCCCCCCHHHHHHHHHHHHH----HHCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCC
Q ss_conf 66654461111464879999999999864----31112347720010232024688878886335788861530110120
Q gi|254781170|r 240 QGTSQLSPYLSIGVLSPRQCWNRLKEEFV----DLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIE 315 (483)
Q Consensus 240 ~~tSrLSPyL~~G~IS~R~v~~~~~~~~~----~~~~~~~~~~~~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~ 315 (483)
..||-||||||||.||+|.||+-++-... +......++..-|++.++-|||.+++++++|.. .+++.....+.+|
T Consensus 237 ~~tsllsP~lhfGe~svr~vf~~~r~~q~~W~~~~~~~~ees~~lfl~~iGlreysry~~fn~P~~-he~~ll~~l~~fP 315 (481)
T TIGR02766 237 ASTSLLSPYLHFGEVSVRKVFQLVRMKQIVWANEGNSEAEESVDLFLRSIGLREYSRYLSFNFPFT-HEKSLLGHLKFFP 315 (481)
T ss_pred CCHHHCCCCHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHHHHHCCCCCC-CHHHHHHHHCCCC
T ss_conf 100000321120203578899888887765311352025688888887502134433321137752-0157885210265
Q ss_pred HHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEE
Q ss_conf 00104678998722788868899999999716763589999999999841047002233477664133111474561002
Q gi|254781170|r 316 WNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWA 395 (483)
Q Consensus 316 w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~ 395 (483)
|.-|++.|++|.+|+||||+||||||||.+|||||||.|.+|+||++|-|.++|++|.+||.+.|+|.|..+...||||+
T Consensus 316 W~~~~~~fk~WrqG~tGyPlvdaGmrelWatGW~h~rirv~~ssf~vk~l~lPW~WGmkyfWd~lldadle~d~lGWqyi 395 (481)
T TIGR02766 316 WKVDEEKFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFAVKVLLLPWRWGMKYFWDTLLDADLESDILGWQYI 395 (481)
T ss_pred CHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCHHCCEEE
T ss_conf 11203555554068888840343357776504200202102445778887343021157888887630010000010012
Q ss_pred EECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHHHHH------CCCCCCCCCCCCCHHHHHHH
Q ss_conf 012789847022046458988724899783300824327997780495540131------25789999763189999999
Q gi|254781170|r 396 ASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDK------NDLSLNYPLPIVDHKKACHH 469 (483)
Q Consensus 396 a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~~~~------~~~~~~YP~pivd~~~~~~~ 469 (483)
+|+-.|+...-|+-||..|+.||||+|+|||+|+|||+.+|+++||.||.+|.. .++|.+||.||||+..|++.
T Consensus 396 ~G~lPd~~el~r~dnP~~~G~k~dP~G~y~r~WlPel~rlPt~WihhPW~aP~~~l~~~GvelG~ny~~Piv~l~~a~~~ 475 (481)
T TIGR02766 396 SGSLPDGRELDRLDNPQLEGAKYDPEGEYVRRWLPELARLPTEWIHHPWDAPESVLKAAGVELGSNYPKPIVDLDAARER 475 (481)
T ss_pred ECCCCCCCHHHHCCCCCCCCCEECCCCHHHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf 12578720001115633366114787313765303654067224047632157899750201034455420117899999
Q ss_pred HHHH
Q ss_conf 9999
Q gi|254781170|r 470 TLNQ 473 (483)
Q Consensus 470 a~~~ 473 (483)
-.+.
T Consensus 476 l~~~ 479 (481)
T TIGR02766 476 LDEA 479 (481)
T ss_pred HHHH
T ss_conf 9862
No 8
>TIGR00591 phr2 deoxyribodipyrimidine photolyase; InterPro: IPR008148 Deoxyribodipyrimidine photolyase (DNA photolyase) is a DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), breaks the cyclobutane ring joining the two pyrimidines of the dimer. DNA photolyase is an enzyme that requires two choromophore-cofactors for its activity: a reduced FADH2 and either 5,10-methenyltetrahydrofolate (5,10-MTFH) or an oxidized 8-hydroxy-5- deazaflavin (8-HDF) derivative (F420). The folate or deazaflavin chromophore appears to function as an antenna, while the FADH2 chromophore is thought to be responsible for electron transfer. On the basis of sequence similarities DNA photolyases can be grouped into two classes. The second class contains enzymes from Myxococcus xanthus, methanogenic archaebacteria, insects, fish and marsupial mammals. It is not yet known what second cofactor is bound to class 2 enzymes. There are a number of conserved sequence regions in all known class 2 DNA photolyases, especially in the C-terminal part. ; GO: 0003904 deoxyribodipyrimidine photo-lyase activity, 0006281 DNA repair.
Probab=100.00 E-value=0 Score=374.64 Aligned_cols=397 Identities=21% Similarity=0.259 Sum_probs=285.5
Q ss_pred CEEEEEECCCCCCCCCHHHHHHHHHC---CCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf 42688835867556778999999957---982999997383784788899899999999999999999975980999965
Q gi|254781170|r 8 SVHLVWLRNDLRITDNKALYAACHNS---DAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQC 84 (483)
Q Consensus 8 ~~~IvWfRrDLRl~DN~aL~~A~~~~---~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~ 84 (483)
..-|||+.||-|++||+||.+|.+.+ +.|+..|||+-|.+. ++..||..||+++|.|+.++|+++|++|++..
T Consensus 23 g~vvYWM~rd~Rv~DNWAL~yA~~LA~~~~~PL~VvFcL~p~fl---~A~~RhY~Fml~GL~~v~~~c~~l~Ipf~Ll~- 98 (471)
T TIGR00591 23 GYVVYWMSRDQRVQDNWALIYAQRLALKLKLPLHVVFCLVPKFL---NATIRHYKFMLKGLREVAKECRALGIPFHLLL- 98 (471)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC---CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEC-
T ss_conf 75488740376322579999999999740798699830777876---66517899999999999999986489879757-
Q ss_pred CCCC-CHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCCH---H
Q ss_conf 7535-08999999998709761421001110011001026888752000000223434555760023786443210---1
Q gi|254781170|r 85 SNFD-DSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYT---P 160 (483)
Q Consensus 85 ~~~g-~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~~~~~~~~~~~~l~~p~~i~~~~~~~~~vft---p 160 (483)
| ++.+.|+++++..++.+|+++..+.-...+--..+.+.+...|.+..++.++++|.+.+-+. .-|...| .
T Consensus 99 ---gr~~~~~lP~f~~~~~~~a~VtDf~PL~~~~~w~~~v~k~Lp~~vPl~qVDAhnvVP~w~AS~K--~EY~ArTiR~K 173 (471)
T TIGR00591 99 ---GRSAKEVLPKFVQERDAGAVVTDFSPLRIIRQWVEEVAKALPKDVPLVQVDAHNVVPMWVASDK--LEYSARTIRGK 173 (471)
T ss_pred ---CCCCHHHHHHHHHHCCCCEEECCCCHHHHHHHHHHHHHCCCCCCCCEEEECCCCEECHHHCCCH--HHHHHHHHHHH
T ss_conf ---8986665588885417752653630223107789998504732166256547540031001660--23333545678
Q ss_pred HHHHHHHHCC-CCCCCCCCCC--------CCCCCCCCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCCCCC----CCCC
Q ss_conf 4799886315-6632212455--------44567766755575323476-4345546-88876433322111----1111
Q gi|254781170|r 161 FRKALIQNLV-QADLRSLPVP--------AIRLTGPVTPSNIPRFFDYP-FQAIDPM-FPIGEQNALHILRK----FCKE 225 (483)
Q Consensus 161 f~k~~~~~~~-~~~~~~~p~~--------~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~gGe~~A~~~L~~----Fl~~ 225 (483)
..+.+.+.+. +-|....+.. .......+.....-.....+ .+..+.. .+||+++|+..|.+ ||.+
T Consensus 174 I~~~L~~fL~r~~P~~~~~~~~~Grkle~~~~~~~~vdw~~~~~~l~~dG~~V~E~~~a~pG~~agl~~L~~nkdGF~~~ 253 (471)
T TIGR00591 174 IKKLLPEFLTREFPLVAVHPAAAGRKLEPSLKTAKAVDWEEALASLQVDGREVAEVQWAKPGTKAGLEMLQSNKDGFISQ 253 (471)
T ss_pred HHHHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf 88741442023577556786553553573213367767789999716898838860000684389999987201331666
Q ss_pred CCCHHHHCCCCCCC-CCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCC-HHHHHHHHHHHH--HHH
Q ss_conf 01101202686545-66654461111464879999999999864311123477200102320-246888788863--357
Q gi|254781170|r 226 KVYYYVEQRDIPAI-QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELI-WREFYRHLMAFY--PSV 301 (483)
Q Consensus 226 ~l~~Y~~~Rn~p~~-~~tSrLSPyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~eL~-WRef~~~~~~~~--P~~ 301 (483)
||..|.+.||+|.. ++-|.||||||||+||+.+|..++.+. ......++..|+.||+ +||...++|++. |+.
T Consensus 254 RL~~f~~~RNdP~~p~aLS~LSP~lHfGq~Saqr~al~a~r~----R~~~~~sv~~FlEEL~VRREL~dNFCfY~PG~~Y 329 (471)
T TIGR00591 254 RLELFETDRNDPNKPDALSNLSPWLHFGQLSAQRAALEARRA----RGNSSASVDAFLEELIVRRELADNFCFYNPGPSY 329 (471)
T ss_pred HHHCCCCCCCCCCCHHHHHCCCCHHHHCCCCHHHHHHHHHHH----CCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCC
T ss_conf 640014678887502565247612340443588999999973----0678335776556566544420562240788874
Q ss_pred HHHHHC---------CHHHHCCCHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf 888615---------30110120001046789987227888688999999997167635899999999998410470022
Q gi|254781170|r 302 CMGKPF---------IPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIG 372 (483)
Q Consensus 302 ~~~~~~---------~~~~~~~~w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g 372 (483)
..-++. ...-|..+..++.+.|| +|+|..|++||||+||+.+|.||+.|||- -.|= -+-|..+
T Consensus 330 ds~~gl~~WA~~TL~~H~kD~Re~~YSleqLE---~a~T~D~LWNAAQ~elV~~GKmHGfLRMY----WaKK-ILEWT~~ 401 (471)
T TIGR00591 330 DSLKGLYEWAQKTLMDHAKDKREHLYSLEQLE---KAKTHDPLWNAAQLELVEEGKMHGFLRMY----WAKK-ILEWTAS 401 (471)
T ss_pred CCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHH---CCCCCCHHHHHHHHHHHHCCCCCCCHHHH----HHCE-ECCCCCC
T ss_conf 43356627899998754216877301289730---64676610569999998707603213665----5021-0026887
Q ss_pred ---HHHHHHHH-----HCC-CHHCCCCCCCEEEECCCCCCCC--------CCCCCHHHHHHHHCCCCCEEHCC
Q ss_conf ---33477664-----133-1114745610020127898470--------22046458988724899783300
Q gi|254781170|r 373 ---EEYFMSQL-----LDG-DLASNNGGWQWAASTGNDSVPY--------FRIFNPTIQGKRFDPQGTFIRHW 428 (483)
Q Consensus 373 ---~~~f~~~l-----lD~-d~~~n~~~wq~~a~~G~d~~~~--------~Ri~np~~q~~~~Dp~g~~ir~w 428 (483)
|-=++=+| ||+ ||+ -+.|-.|+- ||+.-+++ +|-+|=.--..||| =.+||+||
T Consensus 402 PeeAL~~aiyLNDrY~~DGrDPn-GyvGcMWsi-CG~HD~gW~ER~iFGKvRyMNy~GckRKF~-v~~y~~r~ 471 (471)
T TIGR00591 402 PEEALSIAIYLNDRYELDGRDPN-GYVGCMWSI-CGIHDQGWAEREIFGKVRYMNYAGCKRKFN-VAEYVRRY 471 (471)
T ss_pred HHHHHHHHHHHCCCCEECCCCCC-CCEEEEEEE-CCCCCCCCCCCCCCCCCCCCCHHHHHHHCC-HHHHHHCC
T ss_conf 68999999985453022674887-601312222-673587644530146413564022332125-25663139
No 9
>pfam00875 DNA_photolyase DNA photolyase. This domain binds a light harvesting cofactor.
Probab=100.00 E-value=2.3e-40 Score=276.41 Aligned_cols=156 Identities=38% Similarity=0.631 Sum_probs=147.9
Q ss_pred EEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCC
Q ss_conf 68883586755677899999995798299999738378478889989999999999999999997598099996575350
Q gi|254781170|r 10 HLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDD 89 (483)
Q Consensus 10 ~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g~ 89 (483)
.||||||||||+||+||.+|++.++ +|+||||+||.+++.+..|++|.+|+++||.+|+++|+++|++|+++. |+
T Consensus 1 vl~WfR~DLRl~DN~aL~~A~~~~~-~v~~vfi~dp~~~~~~~~~~~r~~fl~~sL~~L~~~L~~~g~~L~v~~----g~ 75 (164)
T pfam00875 1 VLVWFRRDLRLHDNPALAAAAASGA-PVIPVFILDPAQLGSHKLGAARRWFLLESLADLDESLAKLGIPLIVRR----GD 75 (164)
T ss_pred CEEEECCCCCHHHHHHHHHHHHCCC-CEEEEEEEEHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEECC----CC
T ss_conf 9899689876302899999997299-789999972677247887889999999999999999996688631058----98
Q ss_pred HHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHH-HCCCCEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 899999999870976142100111001100102688875-2000000223434555760023786443210147998863
Q gi|254781170|r 90 SIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQ-HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQN 168 (483)
Q Consensus 90 ~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~-~~~~~~~~~~~~l~~p~~i~~~~~~~~~vftpf~k~~~~~ 168 (483)
+.++|.+++++++|+.||+|++|++++++||+.|++.|+ .++.++.+++++|++|++++++.|++|+|||||+|+|++.
T Consensus 76 ~~~~l~~l~~~~~i~~v~~n~~~~~~~~~rd~~v~~~l~~~~i~~~~~~~~~L~~p~~i~~~~g~~~~vFTpf~k~~~~~ 155 (164)
T pfam00875 76 PAEVLPELAKELGASAVYWNRDYEPYERRRDAAVKEALREAGIEVHSFDDHLLVPPGEVLTKKGEPYKVFTPFWKAWLKE 155 (164)
T ss_pred HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEECCEEECCCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 58999999996799999991678989999999999999854746999789587775812179849898564899999841
Q ss_pred CC
Q ss_conf 15
Q gi|254781170|r 169 LV 170 (483)
Q Consensus 169 ~~ 170 (483)
..
T Consensus 156 ~~ 157 (164)
T pfam00875 156 LL 157 (164)
T ss_pred CC
T ss_conf 89
No 10
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=99.92 E-value=9e-24 Score=170.87 Aligned_cols=402 Identities=18% Similarity=0.260 Sum_probs=256.7
Q ss_pred EEEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC
Q ss_conf 26888358675567789999999579829999973837847888998999999999999999999759809999657535
Q gi|254781170|r 9 VHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFD 88 (483)
Q Consensus 9 ~~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g 88 (483)
++++|.=-|-=.++++||.. ..+ .+..|.|-.-...........+..+...+++.+...|+..|....+...++ .
T Consensus 3 ~~~~lvLgdQL~~~~~al~~--d~~--~~~vllvE~~~~a~~~r~HkqKl~lv~aAMR~Fad~LraeG~~V~Y~~~~~-~ 77 (505)
T COG3046 3 SSVVLVLGDQLSEDHSALGD--DRS--QDGVLLVESAAEARYRRHHKQKLVLVFAAMRHFADELRAEGLKVRYERADD-N 77 (505)
T ss_pred CEEEEEECCCCCCCCCHHCC--CCC--CCCEEEEHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCC-C
T ss_conf 13899745523555531104--766--673898615767666300612447789999999999862775269997377-6
Q ss_pred CHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHH-HHCCCCEECC-CCCCCCCCCCCCCCC-CCCCCCHHHHHHH
Q ss_conf 089999999987097614210011100110010268887-5200000022-343455576002378-6443210147998
Q gi|254781170|r 89 DSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL-QHRVICKSFD-DSVLLPPGSILNHAL-QMYKVYTPFRKAL 165 (483)
Q Consensus 89 ~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l-~~~~~~~~~~-~~~l~~p~~i~~~~~-~~~~vftpf~k~~ 165 (483)
+....|...++.+..+.|+..+ |.+..-...++++. .-++.+.... .+.|..+.++..-.+ ...-.-.+||+..
T Consensus 78 ~~~~~l~~~l~~~~~d~~~~~~---p~~~~l~~~m~~L~~~~g~~i~~~~~~~Fl~s~a~f~~w~~~~k~~lme~FYr~m 154 (505)
T COG3046 78 SFGGELRRALEAYPGDRVQVQE---PGDHRLEARMKSLSMALGIEITEVENPHFLCSRAEFDAWAGDRKPLLMESFYRRM 154 (505)
T ss_pred CCCHHHHHHHHHCCCCEEEEEC---CCCHHHHHHHHHHHHHCCCEEEEECCCCEECCHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf 4426999999716877579966---7631289999866654382257753755312787766661668541059999998
Q ss_pred HHHC---CCCC-------------CCCCCCCCCCCCCCC--CCC--------CCCCCCCCCC-CCCCCCCCCCCCCCCCC
Q ss_conf 8631---5663-------------221245544567766--755--------5753234764-34554688876433322
Q gi|254781170|r 166 IQNL---VQAD-------------LRSLPVPAIRLTGPV--TPS--------NIPRFFDYPF-QAIDPMFPIGEQNALHI 218 (483)
Q Consensus 166 ~~~~---~~~~-------------~~~~p~~~~~~~~~~--~~~--------~~~~~~~~~~-~~~~~~~~gGe~~A~~~ 218 (483)
.+.. +..+ -...| |....+.+. .++ -+.+.++..+ +...-.||..+++|...
T Consensus 155 Rkr~g~LM~~dqP~GGrWnFDaeNR~~~~-pdL~~P~pl~fppd~~vq~v~e~Ve~~f~~~~G~~e~F~wpvtr~~A~~~ 233 (505)
T COG3046 155 RKRTGILMEDDQPEGGRWNFDAENRKKLP-PDLLPPKPLKFPPDEIVQEVKERVERLFPDNFGQVEGFGWPVTRTQALRA 233 (505)
T ss_pred HHHHCEECCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 88615211379777886776732356799-76789998878996036999999996479998762337897788999999
Q ss_pred CCCCCCCCCCHHHHCCCCCCCC----CCCCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCCC-CHHHHHHH
Q ss_conf 1111111011012026865456----665446111146487999999999986431112347720010232-02468887
Q gi|254781170|r 219 LRKFCKEKVYYYVEQRDIPAIQ----GTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNEL-IWREFYRH 293 (483)
Q Consensus 219 L~~Fl~~~l~~Y~~~Rn~p~~~----~tSrLSPyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~eL-~WRef~~~ 293 (483)
|++|++.++.++....|....+ ..|.|||||+.|.|+|.+|..++.+++.+ ...+-+++|+|++|+ +||||.+.
T Consensus 234 L~~Fi~~~L~nFG~yQDam~~d~~~L~HSllS~alNigLL~PleVi~Aa~~Ay~~-g~ipLN~VEGFvRQiiGWREfmRg 312 (505)
T COG3046 234 LKHFIADRLPNFGSYQDAMSADDPHLWHSLLSFALNIGLLTPLEVIRAALKAYRE-GDIPLNSVEGFVRQIIGWREFMRG 312 (505)
T ss_pred HHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999998631577477787468851578777787632479889999999973235-888668888999998509999877
Q ss_pred HHHHH-HHHHHHHHCCHHHHCCCHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf 88863-35788861530110120001046789987227888688999999997167635899999999998410470022
Q gi|254781170|r 294 LMAFY-PSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIG 372 (483)
Q Consensus 294 ~~~~~-P~~~~~~~~~~~~~~~~w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g 372 (483)
+.+.- |+... .++......+| ..+ | +|+|+.--++-+..+-..+||-|+--|.||.|=+.--+++|-...
T Consensus 313 iY~~~~P~y~t-rN~f~~d~~Lp-----~~y--w-~g~T~M~cl~~av~~v~d~gYAHHIqRLMV~gNfALl~G~dPd~v 383 (505)
T COG3046 313 IYWLKMPDYAT-RNFFNADRKLP-----PFY--W-TGQTKMACLAIAVGRVLDHGYAHHIQRLMVTGNFALLLGVDPDAV 383 (505)
T ss_pred HHHHCCCCHHH-HHHHCCCCCCC-----CCC--C-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 65324885443-12213689999-----744--5-687674289999999861027999999999734788747878999
Q ss_pred HHHHHHHHHC-CCHH---CCCCCCCEEEECCCC-CCCCC------CCCCHHHHHHHHCCCCCEEHCCCH
Q ss_conf 3347766413-3111---474561002012789-84702------204645898872489978330082
Q gi|254781170|r 373 EEYFMSQLLD-GDLA---SNNGGWQWAASTGND-SVPYF------RIFNPTIQGKRFDPQGTFIRHWLP 430 (483)
Q Consensus 373 ~~~f~~~llD-~d~~---~n~~~wq~~a~~G~d-~~~~~------Ri~np~~q~~~~Dp~g~~ir~wvP 430 (483)
-+||+..++| ||+- +-.|.=|++-| |.. ..||. --++-.-++-.|||+..-=.+|||
T Consensus 384 ~~Wf~~~fiDAYdWV~~PNv~GM~qFADG-G~iatKPYasS~nYInkMSDyC~~C~yd~k~r~Gd~aCp 451 (505)
T COG3046 384 DRWFMEVFIDAYDWVELPNVRGMSQFADG-GLIATKPYASSGNYINKMSDYCSDCAYDPKSRLGDDACP 451 (505)
T ss_pred HHHHHHHHHHHHHHEECCCCCCHHHCCCC-CEEECCCCCCCHHHHHHHHHHHHHCCCCHHHCCCCCCCC
T ss_conf 99999987127662134563212220368-555247654311688877676541356803125765576
No 11
>pfam04244 DPRP Deoxyribodipyrimidine photo-lyase-related protein. This family appears to be related to pfam00875.
Probab=97.41 E-value=0.011 Score=36.75 Aligned_cols=140 Identities=12% Similarity=0.165 Sum_probs=93.6
Q ss_pred CCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCC---CCCHHHHHHHH
Q ss_conf 677899999995798299999738378478889989999999999999999997598099996575---35089999999
Q gi|254781170|r 21 TDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSN---FDDSIEWLDSY 97 (483)
Q Consensus 21 ~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~---~g~~~~~L~~l 97 (483)
.+|++|.. .......+.|-++...........+..|++-|+++..++|++.|....++..+. .+...+.|.++
T Consensus 11 ~~~~~l~~----~~~~~~v~miE~~~~~~~~~~HkqKL~l~~sAMRhfa~~L~~~G~~V~Y~~~~~~~~~~~~~~~L~~~ 86 (223)
T pfam04244 11 ADHSALRA----DPDGDLVLMAEVAQEAGYVPHHKQKIALFFSAMRHFAEELRAAGHTVIYLTLDDPDNTGSLPDELARL 86 (223)
T ss_pred CCCHHHHC----CCCCCEEEEEEEHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHH
T ss_conf 98766626----88888899997679946243599999999999999999998669836898666754420189999999
Q ss_pred HHHCCCCCEEEECCCCCHHHHCCHHHHHHHHH-CCCCEECCCC-CCCCCCCCCC--CCCCCCCCCHHHHHHHHHH
Q ss_conf 98709761421001110011001026888752-0000002234-3455576002--3786443210147998863
Q gi|254781170|r 98 CLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH-RVICKSFDDS-VLLPPGSILN--HALQMYKVYTPFRKALIQN 168 (483)
Q Consensus 98 ~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~-~~~~~~~~~~-~l~~p~~i~~--~~~~~~~vftpf~k~~~~~ 168 (483)
+++++++.|.+ ++|....-.+.+.++++. ++.+..+.+. .|..+.+... ...+.+. -..||+...+.
T Consensus 87 l~~~~~~~l~~---~ep~d~~~~~~l~~~~~~~~i~l~~~~sp~FL~s~~~f~~~~~~~K~~~-Me~FYr~~Rk~ 157 (223)
T pfam04244 87 LEEHGIERFEY---TEPGEYRLEQQLKELAESLGIPVEILDDEHFLTSRDEFEAWAKGRKQLR-MEYFYREMRKR 157 (223)
T ss_pred HHHCCCCEEEE---EECCCHHHHHHHHHHHHHCCCCEEECCCCCEECCHHHHHHHHCCCCCHH-HHHHHHHHHHH
T ss_conf 99759987999---8058889999999999846987188799985337999998642487355-99999999987
No 12
>KOG0133 consensus
Probab=91.96 E-value=0.0052 Score=38.78 Aligned_cols=133 Identities=13% Similarity=0.020 Sum_probs=69.5
Q ss_pred CCCCCCCCCCC---CCCCCCCCHHHHCCCCCC-CCCCCCCC--HHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCC
Q ss_conf 87643332211---111110110120268654-56665446--1111464879999999999864311123477200102
Q gi|254781170|r 210 IGEQNALHILR---KFCKEKVYYYVEQRDIPA-IQGTSQLS--PYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLN 283 (483)
Q Consensus 210 gGe~~A~~~L~---~Fl~~~l~~Y~~~Rn~p~-~~~tSrLS--PyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~ 283 (483)
.++..|..... -++...+..+...+|.+. ...++.++ |+|.+|+++.++.-....... ....+..++-.
T Consensus 300 ~~y~~~~n~p~~~~m~~n~~~~~ipw~~n~~~~~aw~~G~tG~P~ida~m~~l~~~gw~h~~~R-----~~vasf~tr~~ 374 (531)
T KOG0133 300 FFYTAAFNTPYFDDMPGNKILLQIPWDKNPPKLAAWLEGLTGYPWLDAGMRQLLASGWEHHRSR-----TIVASFLTRGD 374 (531)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCC-----HHHHHHHHCCC
T ss_conf 4567512785424564554212387555715557887078899734599999999888753231-----13576740351
Q ss_pred CCC-HHHHHHHHHHHHHHHHHHHHC---------CHHHHCCCHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCC
Q ss_conf 320-246888788863357888615---------3011012000104678998722788868899999999716763
Q gi|254781170|r 284 ELI-WREFYRHLMAFYPSVCMGKPF---------IPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMH 350 (483)
Q Consensus 284 eL~-WRef~~~~~~~~P~~~~~~~~---------~~~~~~~~w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mh 350 (483)
.++ |||-..+++.+-.+-....+. ....+++.-.+++..+. .+-|--++.++..-+....|=||
T Consensus 375 L~i~w~eg~~~F~~~llD~D~~~~agnW~~~S~~s~f~~~~~~~ysp~~~~---kk~dP~g~yir~~lp~l~~~p~~ 448 (531)
T KOG0133 375 LLISWREGLDVFMEYLLDADSSKNAGNWMWLSSTSHFFDQFDRVYSPVALG---KKLDPDGLYIRQWLPELRSGPMH 448 (531)
T ss_pred EEEEHHHHHHHHHHHHCCHHHHCCCCCCCEECCCCCCCCCCCCCCCHHHHH---CCCCCCHHHHHHHHHHHHCCCCC
T ss_conf 132389899999987336043238776541226640014666133899982---76796412588871998618861
No 13
>TIGR02963 xanthine_xdhA xanthine dehydrogenase, small subunit; InterPro: IPR014307 Members of this protein are the small subunit (or, in eukaryotes, the N-terminal domain) of xanthine dehydrogenase, an enzyme of purine catabolism via urate. The small subunit contains both an FAD and a 2Fe-2S cofactor. Aldehyde oxidase (retinal oxidase) appears to have arisen as a neofunctionalisation among xanthine dehydrogenases in eukaryotes. ; GO: 0004854 xanthine dehydrogenase activity, 0004855 xanthine oxidase activity, 0050660 FAD binding.
Probab=81.95 E-value=0.84 Score=24.71 Aligned_cols=65 Identities=11% Similarity=0.098 Sum_probs=33.4
Q ss_pred HHHHHHHH-HHHHHHHHH----HHHCCCEE--EEEECCCCCCHHHHHHHHHHHCCCCCEEE-ECCCCCHHHHCCHHHHH
Q ss_conf 89999999-999999999----99759809--99965753508999999998709761421-00111001100102688
Q gi|254781170|r 55 ARQSHFIY-ASLLQVQKS----LSQKGIVF--QYHQCSNFDDSIEWLDSYCLQQRVTKLFY-NRQYEINEVRRDKLLEK 125 (483)
Q Consensus 55 ~~~~~Fl~-esL~~L~~~----L~~~g~~L--~v~~~~~~g~~~~~L~~l~~~~~i~~v~~-n~~~~~~~~~rd~~i~~ 125 (483)
......+. +.|+.++.. |..-+..+ ++ -..++.|.+|..++.-.+|.. +.|.+.+-.+.-+.+..
T Consensus 198 ~~~~~~i~P~~L~~~~~~~~~~l~~~~~~~~W~~------P~t~~dLA~l~~a~P~ArivAGsTDVGLWVTk~~R~L~~ 270 (515)
T TIGR02963 198 DADRAAIIPERLRALRAGETVELNSGGERFTWIA------PTTLDDLAALKAAHPKARIVAGSTDVGLWVTKQMRDLPD 270 (515)
T ss_pred CCHHHHCCHHHHHHHCCCCCEEEECCCCCEEEEE------CCCHHHHHHHHHHCCCCEEEECCEEHHHHHHHHHHHHHC
T ss_conf 0013301028989644798489841786158870------688899999997289958996460046688564211211
No 14
>PRK00768 nadE NAD synthetase; Reviewed
Probab=75.96 E-value=2.9 Score=21.27 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=21.9
Q ss_pred EEECCC---CCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHH---CCCHHHHCCHHH
Q ss_conf 201278---984702204645898872489978330082432---799778049554
Q gi|254781170|r 395 AASTGN---DSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELN---NVPTQYIHAPHS 445 (483)
Q Consensus 395 ~a~~G~---d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~---~~p~~~ih~p~~ 445 (483)
+.|||+ +..+||-.|-= -+-++=|=|..-|.-|=+|+ ++|..-|..|.+
T Consensus 157 VlGTgNksE~~vGYfTkYGD--g~~Di~PI~dL~KteV~~lA~~LgvP~~Ii~k~PS 211 (274)
T PRK00768 157 VVGTDHAAEAITGFFTKFGD--GGADLLPLFGLNKRQGRALLAALGAPEHLYEKVPT 211 (274)
T ss_pred EECCCCHHHHHCCCEEEECC--CCCCHHHHCCCCHHHHHHHHHHHCCCHHHHCCCCC
T ss_conf 86488640444085010267--75173763256199999999995979998368989
No 15
>pfam11940 DUF3458 Domain of unknown function (DUF3458). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 402 to 419 amino acids in length. This domain is found associated with pfam01433. This domain has a conserved FSAPV sequence motif.
Probab=74.89 E-value=2.3 Score=21.94 Aligned_cols=93 Identities=24% Similarity=0.419 Sum_probs=62.5
Q ss_pred CHHCCHHHHHHHHHCCCCCCHHHH--HHHHHHHH-CC---CCHHHHHHHHHHHHHH-HCCCHHHHH--HHHHHHHHCCCH
Q ss_conf 000104678998722788868899--99999971-67---6358999999999984-104700223--347766413311
Q gi|254781170|r 315 EWNKDSHLLQAWKQGYTGFPIIDA--AMRQLNTI-GW---MHNRLRMITASFLVKD-LLVDWRIGE--EYFMSQLLDGDL 385 (483)
Q Consensus 315 ~w~~~~~~~~aW~~G~TG~PlVDA--~MR~L~~t-G~---mhnr~Rm~vaSfl~~~-L~idWr~g~--~~f~~~llD~d~ 385 (483)
+|.+|.-.+++|=.=+-+-|.-|+ -.+.|.+. -| -.||+|.++++|...| ...|=.-|+ +++++.++.-|.
T Consensus 276 ~w~~d~LV~dkWF~~qA~~~~~~~l~~V~~L~~Hp~F~~~NPNrvRalig~Fa~~N~~~FH~~dG~GY~flad~i~~ld~ 355 (408)
T pfam11940 276 RWKDDPLVMDKWFALQASSPRPDALERVKALMQHPAFDLKNPNRVRALIGAFAAANPAGFHAADGSGYRFLADQIIKLDP 355 (408)
T ss_pred HHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCHHHHHCCCCCHHHHHHHHHHHHCC
T ss_conf 87669399999999984388998899999996598878569938999999998449186738999689999999998747
Q ss_pred HCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCC
Q ss_conf 147456100201278984702204645898872489
Q gi|254781170|r 386 ASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQ 421 (483)
Q Consensus 386 ~~n~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~ 421 (483)
-+= |-+| |+-.|..+=++|||.
T Consensus 356 ~NP----qvAA----------Rl~~~f~~w~~~d~~ 377 (408)
T pfam11940 356 VNP----QVAA----------RLLTPFSRWRRYDPK 377 (408)
T ss_pred CCH----HHHH----------HHHHHHHHHHHCCHH
T ss_conf 586----9999----------999998889853898
No 16
>COG1087 GalE UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]
Probab=71.15 E-value=3.3 Score=20.94 Aligned_cols=16 Identities=6% Similarity=0.198 Sum_probs=12.2
Q ss_pred HHHHHHHHHCCCCCEE
Q ss_conf 9999999870976142
Q gi|254781170|r 92 EWLDSYCLQQRVTKLF 107 (483)
Q Consensus 92 ~~L~~l~~~~~i~~v~ 107 (483)
+.|.++.++++|+.|+
T Consensus 57 ~~L~~vf~~~~idaVi 72 (329)
T COG1087 57 ALLTAVFEENKIDAVV 72 (329)
T ss_pred HHHHHHHHHCCCCEEE
T ss_conf 9999999864998899
No 17
>pfam04104 DNA_primase_lrg Eukaryotic and archaeal DNA primase, large subunit. DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae). The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase.
Probab=69.03 E-value=8.6 Score=18.30 Aligned_cols=63 Identities=21% Similarity=0.190 Sum_probs=42.3
Q ss_pred CCCCCHHHHHHHHH----HHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH----CCCHHCCCCCCCEEEE
Q ss_conf 78886889999999----97167635899999999998410470022334776641----3311147456100201
Q gi|254781170|r 330 YTGFPIIDAAMRQL----NTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLL----DGDLASNNGGWQWAAS 397 (483)
Q Consensus 330 ~TG~PlVDA~MR~L----~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~ll----D~d~~~n~~~wq~~a~ 397 (483)
..-||. |||.| ...+-+.+-+|+.+++|| |+++++=.....+|.+.+. |||-. -.-|.....|
T Consensus 97 ~~~fPp---Cm~~~~~~l~~~~~l~h~~R~~l~~FL-k~iG~~~~e~l~~~~~~f~k~~~~f~k~-~~Y~i~H~yG 167 (217)
T pfam04104 97 PEHFPP---CMRNLLEGLRAGGHLKHEGRFQLTLFL-KGIGLSLDEILEFWREAFTRTSPDFDKE-YRYNIRHNYG 167 (217)
T ss_pred HHHCCH---HHHHHHHHHHCCCCCCCHHHHHHHHHH-HHCCCCHHHHHHHHHHHCCCCCCCCCCC-CCCEEEECCC
T ss_conf 641889---999999999717887842599999999-8679989999999997314688864413-6651364047
No 18
>TIGR01488 HAD-SF-IB HAD-superfamily hydrolase, subfamily IB (PSPase-like); InterPro: IPR006383 This group represents a subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. Subfamily IA, B, C and D are distinguished from the rest of the superfamily by the presence of a variable domain between the first and second conserved catalytic motifs. In subfamilies IA and IB, this domain consists of an alpha-helical bundle. It was necessary to model these two subfamilies separately, breaking them at an apparent phylogenetic bifurcation, so that the resulting model(s) are not so broadly defined that members of subfamily III (which lack the variable domain) are included. ; GO: 0016791 phosphoric monoester hydrolase activity, 0008152 metabolic process.
Probab=68.60 E-value=8.8 Score=18.24 Aligned_cols=70 Identities=13% Similarity=0.136 Sum_probs=48.6
Q ss_pred EEEEEEECHHHHCC---CCC-CHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCCCCC----EEE
Q ss_conf 99999738378478---889-9899999999999999999975980999965753508999999998709761----421
Q gi|254781170|r 37 VIAVFIATPEQWRQ---HGI-SARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTK----LFY 108 (483)
Q Consensus 37 vlpvyi~dp~~~~~---~~~-~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~----v~~ 108 (483)
.+.|.+-....+.. ... ......|++....++-+.+++.|..+.|.. |.+.-.+..++..+++.. |++
T Consensus 61 ~~~i~v~~~~~~~~a~~~~~~~~~~~~r~~~~~~~~~~~~~~~G~~~~ivS----gg~~~~~~~~~e~~g~~~~F~~~~~ 136 (204)
T TIGR01488 61 FLEIKVDAKEELAKAVEEFLAKEVAIDRLYPGARELIKWLKEKGIKTVIVS----GGLDFLVEPLAEKLGVDEVFKEVYA 136 (204)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCHHHCCHHHHHHHHHHHHCCCCEEEEC----CCHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 356114558889888998886411013225308999999984799299980----8867999999975284344322232
Q ss_pred EC
Q ss_conf 00
Q gi|254781170|r 109 NR 110 (483)
Q Consensus 109 n~ 110 (483)
|+
T Consensus 137 ~~ 138 (204)
T TIGR01488 137 NE 138 (204)
T ss_pred HE
T ss_conf 00
No 19
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=64.00 E-value=11 Score=17.68 Aligned_cols=71 Identities=17% Similarity=0.201 Sum_probs=46.8
Q ss_pred HHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEC
Q ss_conf 95798299999738378478889989999999999999999997598099996575350899999999870976142100
Q gi|254781170|r 31 HNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNR 110 (483)
Q Consensus 31 ~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~v~~n~ 110 (483)
+.-++++..|||..|... ..+...... |.++.+-.+++|....+..+ +++.+.|.+++++.+++.|+.-+
T Consensus 24 ~~~~a~l~vl~V~~~~~~---~~~~~~~~~----l~~~~~la~~lga~~~~~~~---~d~~~~I~~~A~~~~~t~IVlG~ 93 (124)
T cd01987 24 DRLKAPWYVVYVETPRLN---RLSEAERRR----LAEALRLAEELGAEVVTLPG---DDVAEAIVEFAREHNVTQIVVGK 93 (124)
T ss_pred HHCCCCEEEEEEECCCCC---CCCHHHHHH----HHHHHHHHHHCCCEEEEEEC---CCHHHHHHHHHHHCCCCEEEECC
T ss_conf 964998999999559756---589799999----99999999985998999947---99899999999984998999768
Q ss_pred C
Q ss_conf 1
Q gi|254781170|r 111 Q 111 (483)
Q Consensus 111 ~ 111 (483)
.
T Consensus 94 ~ 94 (124)
T cd01987 94 S 94 (124)
T ss_pred C
T ss_conf 9
No 20
>pfam05268 GP38 Phage tail fibre adhesin Gp38. This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, gp57, catalyses the organisation of gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition.
Probab=60.45 E-value=3.4 Score=20.84 Aligned_cols=13 Identities=8% Similarity=0.207 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999999999
Q gi|254781170|r 57 QSHFIYASLLQVQ 69 (483)
Q Consensus 57 ~~~Fl~esL~~L~ 69 (483)
-..||-.+.++|+
T Consensus 19 GqrWM~~Aa~~lR 31 (261)
T pfam05268 19 GQRWMDAAARRLR 31 (261)
T ss_pred CCHHHHHHHHHHH
T ss_conf 4278999987650
No 21
>cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.
Probab=60.07 E-value=13 Score=17.23 Aligned_cols=86 Identities=13% Similarity=0.101 Sum_probs=47.8
Q ss_pred CHHHHHHH---HHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf 78999999---957982999997383784788899899999999999999999975980999965753508999999998
Q gi|254781170|r 23 NKALYAAC---HNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCL 99 (483)
Q Consensus 23 N~aL~~A~---~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~ 99 (483)
..+|..|+ ...+..+..|+|.++..............=..+-|..+...+...|........ .|++.+.|.+.++
T Consensus 13 ~~al~~a~~la~~~~~~l~~v~v~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~~a~ 90 (130)
T cd00293 13 ERALRWAARLARRLGAELVLLHVVDPPPSSAAELAELLEEEARALLEALREALAEAGVKVETVVL--EGDPAEAILEAAE 90 (130)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEE--ECCHHHHHHHHHH
T ss_conf 99999999999872997999999728865530144678999999999999985427983899999--4661899988777
Q ss_pred HCCCCCEEEEC
Q ss_conf 70976142100
Q gi|254781170|r 100 QQRVTKLFYNR 110 (483)
Q Consensus 100 ~~~i~~v~~n~ 110 (483)
+.+++-|..-.
T Consensus 91 ~~~~dliV~G~ 101 (130)
T cd00293 91 ELGADLIVMGS 101 (130)
T ss_pred HCCCCEEEEEC
T ss_conf 61188999947
No 22
>TIGR03333 salvage_mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase. Members of this family are the methionine salvage enzyme MnxX, a member of the HAD-superfamily hydrolases, subfamily IB (see TIGR01488). Members are found in Bacillus subtilis and related species, paired with MtnW (TIGR03332). In most species that recycle methionine from methylthioadenosine, the single protein MtnC replaces the MtnW/MtnX pair. In B. subtilis, mtnX was first known as ykrX.
Probab=59.33 E-value=12 Score=17.41 Aligned_cols=15 Identities=7% Similarity=0.200 Sum_probs=6.7
Q ss_pred CCCCHHHHHHHHHHH
Q ss_conf 648799999999998
Q gi|254781170|r 252 GVLSPRQCWNRLKEE 266 (483)
Q Consensus 252 G~IS~R~v~~~~~~~ 266 (483)
|+||.+.++..+.+.
T Consensus 8 GTIT~~D~~~~il~~ 22 (214)
T TIGR03333 8 GTITNNDNIISIMKQ 22 (214)
T ss_pred CCCCCCHHHHHHHHH
T ss_conf 987830559999998
No 23
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=59.29 E-value=3.1 Score=21.14 Aligned_cols=46 Identities=28% Similarity=0.346 Sum_probs=32.0
Q ss_pred HCCCHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHH
Q ss_conf 13311147456100201278984702204645898872489978330082432
Q gi|254781170|r 381 LDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELN 433 (483)
Q Consensus 381 lD~d~~~n~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~ 433 (483)
+|.|.++|||+.-=+-|.-+ .--|+ .||.+||++|....=|.+|=+
T Consensus 476 ~ea~~a~NYGgIGaVIgHEI-----~HgFD--dqGakfD~~GnL~dWWT~eD~ 521 (654)
T COG3590 476 PEADSAANYGGIGAVIGHEI-----GHGFD--DQGAKFDGDGNLNDWWTDEDA 521 (654)
T ss_pred CCCCHHHCCCCCCCEEHHHH-----CCCCC--CCCCCCCCCCCHHHHCCHHHH
T ss_conf 77650104667200000021-----24546--776546999857762578779
No 24
>PRK09552 mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase; Reviewed
Probab=57.30 E-value=11 Score=17.53 Aligned_cols=82 Identities=13% Similarity=0.086 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCC-CCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHCCHHHHHHHHHCC
Q ss_conf 64879999999999864311123477200102-32024688878886335788861530110120001046789987227
Q gi|254781170|r 252 GVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLN-ELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGY 330 (483)
Q Consensus 252 G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~-eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~~~~~aW~~G~ 330 (483)
|+||.+.+...+.+.+..... .+-.+.|+. ++.-||.+..++..-|.-....-..-..++++-+..-..|-.|++.+
T Consensus 11 GTIT~~D~~~~ll~~fa~~~w--~~i~~~~~~g~is~re~~~~~~~~i~~~~~~e~~~~l~~~~~idpgF~eF~~~~~~~ 88 (219)
T PRK09552 11 GTITNNDNIISIMEKFAPPEA--EELKDRILSQELSIQEGVGQMFQLLPTNLKDEIIQFLLETAEIRNGFHEFVQFVNEN 88 (219)
T ss_pred CCCCCHHHHHHHHHHHCHHHH--HHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
T ss_conf 887720638999998592989--999999981986699999999984788627899999995699686799999999985
Q ss_pred CCCCHH
Q ss_conf 888688
Q gi|254781170|r 331 TGFPII 336 (483)
Q Consensus 331 TG~PlV 336 (483)
|+|++
T Consensus 89 -~ip~~ 93 (219)
T PRK09552 89 -NISFY 93 (219)
T ss_pred -CCCEE
T ss_conf -99799
No 25
>pfam03392 OS-D Insect pheromone-binding family, A10/OS-D.
Probab=56.59 E-value=4 Score=20.40 Aligned_cols=14 Identities=21% Similarity=0.826 Sum_probs=10.5
Q ss_pred HHHHCCCCCEEHCC
Q ss_conf 88724899783300
Q gi|254781170|r 415 GKRFDPQGTFIRHW 428 (483)
Q Consensus 415 ~~~~Dp~g~~ir~w 428 (483)
..+|||+|+|.+++
T Consensus 82 ~~KyDP~g~y~~ky 95 (95)
T pfam03392 82 VAKYDPEGEYRKKY 95 (95)
T ss_pred HHHHCCCCCHHHCC
T ss_conf 99759795233219
No 26
>TIGR03531 selenium_SpcS O-phosphoseryl-tRNA(Sec) selenium transferase. In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein.
Probab=56.18 E-value=15 Score=16.82 Aligned_cols=81 Identities=16% Similarity=0.357 Sum_probs=36.7
Q ss_pred HHHHHHHHHHCC--CEEEEEECC-----CCCCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHH-C--CCCE
Q ss_conf 999999999759--809999657-----53508999999998709761421001110011001026888752-0--0000
Q gi|254781170|r 65 LLQVQKSLSQKG--IVFQYHQCS-----NFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH-R--VICK 134 (483)
Q Consensus 65 L~~L~~~L~~~g--~~L~v~~~~-----~~g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~-~--~~~~ 134 (483)
+.++++.++++| ..+.|+... +..|-+..+.++|++++|-+|+-| .|+.....--+.|++..+. + ..++
T Consensus 191 v~~ie~~i~~~g~~~i~cVlSTTScFAPR~~D~i~eiAklC~~~~IpHvVNN-AYGlQ~~~~~~~i~~A~r~GRVDa~VQ 269 (444)
T TIGR03531 191 VEDIERAIEEIGPENILCVLSTTSCFAPRSPDDIEEIAKICAKYDIPHVVNN-AYGLQSNKYMEKINKAIKVGRVDAVVS 269 (444)
T ss_pred HHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCCEEECC-HHHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf 9999999998286764799853654599997669999999997499837842-036617999999999986498319997
Q ss_pred ECCCCCCCCCCC
Q ss_conf 022343455576
Q gi|254781170|r 135 SFDDSVLLPPGS 146 (483)
Q Consensus 135 ~~~~~~l~~p~~ 146 (483)
+.+-++++|.+.
T Consensus 270 StDKNflVPVGG 281 (444)
T TIGR03531 270 STDKNFMVPVGG 281 (444)
T ss_pred ECCCCEEEECCC
T ss_conf 068662543487
No 27
>PRK03980 flap endonuclease-1; Provisional
Probab=55.38 E-value=13 Score=17.12 Aligned_cols=37 Identities=8% Similarity=-0.076 Sum_probs=19.3
Q ss_pred CCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHHCC
Q ss_conf 50899999999870976142100111001100102688875200
Q gi|254781170|r 88 DDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRV 131 (483)
Q Consensus 88 g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~~~ 131 (483)
.+.++.+.++....+|.-|.+ |.+ -|..+...++.+.
T Consensus 82 ~~~i~~~k~LL~~~Gipyi~A-----p~E--Aeaqca~L~~~g~ 118 (295)
T PRK03980 82 DEIVEDSKKLLDLMGIPYVQA-----PSE--GEAQAAYMVKKGD 118 (295)
T ss_pred HHHHHHHHHHHHHCCCCCCCC-----CCH--HHHHHHHHHHCCC
T ss_conf 999999999999869871218-----725--9999999997697
No 28
>PRK09568 DNA primase large subunit; Reviewed
Probab=54.34 E-value=14 Score=16.88 Aligned_cols=47 Identities=6% Similarity=0.009 Sum_probs=33.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCH
Q ss_conf 9999999971676358999999999984104700223347766413311
Q gi|254781170|r 337 DAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDL 385 (483)
Q Consensus 337 DA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~ 385 (483)
=-||++|.+-+=+.+-+|-++||||.+ .+.+=-.-...|... =|+|.
T Consensus 216 PPCi~~l~~g~nL~H~~RFalatfL~~-iG~~vd~I~~lf~~~-pd~~~ 262 (306)
T PRK09568 216 PPCIREIQEKKELNREEARALIVYYIN-IGSSVDSIALVLEKN-GDENL 262 (306)
T ss_pred CCHHHHHHCCCCCCHHHHHHHHHHHHH-CCCCHHHHHHHHHCC-CCHHH
T ss_conf 805999874798882889999999997-599799999998629-92778
No 29
>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio
Probab=54.26 E-value=16 Score=16.62 Aligned_cols=85 Identities=8% Similarity=-0.002 Sum_probs=48.6
Q ss_pred HHHHHH---HHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf 899999---99579829999973837847888998999999999999999999759809999657535089999999987
Q gi|254781170|r 24 KALYAA---CHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQ 100 (483)
Q Consensus 24 ~aL~~A---~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~ 100 (483)
.||..| ++..++.++++.|.++..............=.-+-+..+....+..|.+....... -|++.+.+.+.+++
T Consensus 14 ~al~~A~~la~~~~a~l~~lhVv~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~I~~~a~e 92 (132)
T cd01988 14 DLLELAAALARAQNGEIIPLNVIEVPNHSSPSQLEVNVQRARKLLRQAERIAASLGVPVHTIIRI-DHDIASGILRTAKE 92 (132)
T ss_pred HHHHHHHHHHHHCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEE-CCCHHHHHHHHHHH
T ss_conf 99999999998769989999998458767855667899999999999999998769956999997-79979999999998
Q ss_pred CCCCCEEEE
Q ss_conf 097614210
Q gi|254781170|r 101 QRVTKLFYN 109 (483)
Q Consensus 101 ~~i~~v~~n 109 (483)
.+++-|.+-
T Consensus 93 ~~~DlIVmG 101 (132)
T cd01988 93 RQADLIIMG 101 (132)
T ss_pred HCCCEEEEC
T ss_conf 499999983
No 30
>pfam01902 ATP_bind_4 ATP-binding region. This family of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.In some members of this family, this domain is associated with pfam01042.
Probab=54.10 E-value=16 Score=16.61 Aligned_cols=94 Identities=19% Similarity=0.115 Sum_probs=53.6
Q ss_pred CHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCC-CCCHHHHHHHHHHHC
Q ss_conf 7899999995798299999738378478889989999999999999999997598099996575-350899999999870
Q gi|254781170|r 23 NKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSN-FDDSIEWLDSYCLQQ 101 (483)
Q Consensus 23 N~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~-~g~~~~~L~~l~~~~ 101 (483)
..||+.|.+. ..|.++...-|...+ +..|-.-.+.-++.+-+.+|++|+....+. ..+..+.|.+..+++
T Consensus 14 ~~Al~~a~~~--~~v~~L~t~~~~~~d-------s~~~H~~~~~l~~~qA~algiPl~~~~~~~~~e~~~~~L~~~l~~~ 84 (219)
T pfam01902 14 NYALYWALKE--IEVPYLVSMKSENKE-------SYMFHEPNLHLTKLLAEALGIPIIKLYTKGEEEKEVEDLAGFLESL 84 (219)
T ss_pred HHHHHHHHHC--CCCEEEEEEEECCCC-------CCCCCCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHC
T ss_conf 9999999871--983799999637998-------1026157889999999975996899967986179999999999875
Q ss_pred CCCCEEEECCCCCHHHHCCHHHHHHHH
Q ss_conf 976142100111001100102688875
Q gi|254781170|r 102 RVTKLFYNRQYEINEVRRDKLLEKRLQ 128 (483)
Q Consensus 102 ~i~~v~~n~~~~~~~~~rd~~i~~~l~ 128 (483)
+|+.|.+-.-...+.+.| +++.|.
T Consensus 85 ~i~~vv~GdI~s~~qr~~---~e~~c~ 108 (219)
T pfam01902 85 DVDALVAGAIYSEYQKSR---IESVCR 108 (219)
T ss_pred CCCEEEECCCCCHHHHHH---HHHHHH
T ss_conf 986999986036889999---999999
No 31
>TIGR01187 potA polyamine ABC transporter, ATP-binding protein; InterPro: IPR005893 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family comprises the spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belongs to the larger ATP-Binding Cassette (ABC) transporter superfamily. Polyamines like spermidine and putrescine play a vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included).; GO: 0015417 polyamine-transporting ATPase activity, 0015846 polyamine transport, 0016020 membrane.
Probab=50.61 E-value=15 Score=16.71 Aligned_cols=39 Identities=21% Similarity=0.162 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEECCCC
Q ss_conf 99999999999997598099996575350899999999870976142100111
Q gi|254781170|r 61 IYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYE 113 (483)
Q Consensus 61 l~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~v~~n~~~~ 113 (483)
|-|+|-.|+++|+++ ....|..+..+.+||.||..+|-+
T Consensus 124 lDEpLsALD~kLR~~--------------MQ~ELk~~~~~LGiT~v~VTHDQ~ 162 (331)
T TIGR01187 124 LDEPLSALDKKLRDQ--------------MQLELKTLQEQLGITFVFVTHDQE 162 (331)
T ss_pred ECCCHHHHHHHHHHH--------------HHHHHHHHHHHCCCEEEEEECCHH
T ss_conf 117722643898998--------------899999998726828999701848
No 32
>TIGR00338 serB phosphoserine phosphatase SerB; InterPro: IPR004469 Phosphoserine phosphatase (SerB), (3.1.3.3 from EC), also known as O-phosphoserine phosphohydrolase, is involved in both serine and glycine biosynthesis. It catalyzes the reaction 3-phospho-serine + H2O = L-serine + phosphate, which is the last step in the biosynthesis of serine from carbohydrates. The reaction proceeds via the formation of a phosphoryl-enzyme intermediate. It acts as a homodimer, and requires magnesium as a cofactor.; GO: 0004647 phosphoserine phosphatase activity, 0006564 L-serine biosynthetic process.
Probab=48.82 E-value=19 Score=16.08 Aligned_cols=47 Identities=15% Similarity=0.075 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCCCCC--EEEECC
Q ss_conf 999999999999975980999965753508999999998709761--421001
Q gi|254781170|r 61 IYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTK--LFYNRQ 111 (483)
Q Consensus 61 l~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~--v~~n~~ 111 (483)
|.+++.+|=+.|+++|..+.+..|. ...+-..+..+.+++. +|+|+-
T Consensus 87 L~~G~~Elv~~L~~~gykVav~SGG----F~~~a~~~k~~L~LD~tn~faN~L 135 (223)
T TIGR00338 87 LTEGAEELVKTLKEKGYKVAVISGG----FDLFAEHLKDKLGLDYTNAFANRL 135 (223)
T ss_pred CCCCHHHHHHHHHHCCEEEEEEECC----HHHHHHHHHHHHCCCHHHHHHCEE
T ss_conf 9978789999998869079998577----688898889985788647210200
No 33
>TIGR00273 TIGR00273 iron-sulfur cluster binding protein; InterPro: IPR004452 Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulphur clusters..
Probab=48.24 E-value=20 Score=16.03 Aligned_cols=68 Identities=15% Similarity=0.203 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHH-CCCCEECC
Q ss_conf 999999999975980999965753508999999998709761421001110011001026888752-00000022
Q gi|254781170|r 64 SLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH-RVICKSFD 137 (483)
Q Consensus 64 sL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~-~~~~~~~~ 137 (483)
=|..|++.+.+.|...++-+. -+|+.+++.+++++.++.+|+=.+.--..|+. +.++|+. |+.+.+.|
T Consensus 52 Yl~~~~~~~~~~G~~vYyA~~--~eeA~~ii~~v~~~KN~k~vvK~KSMvsEEI~----Ln~~L~~~G~~v~ETD 120 (450)
T TIGR00273 52 YLEQLKENVTQRGGHVYYAKT--AEEARKIILKVAQEKNGKKVVKSKSMVSEEIG----LNEVLEKKGIEVVETD 120 (450)
T ss_pred HHHHHHHHHHHCCCEEEEECC--HHHHHHHHHHHHHHHCCCEEECCCCCCEEECC----HHHHHHHCCCEEEEEC
T ss_conf 999999999858956987278--78999999998864133442113464000322----1488876597799800
No 34
>pfam04045 P34-Arc Arp2/3 complex, 34 kD subunit p34-Arc. Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. This family represents the p34-Arc subunit.
Probab=46.84 E-value=8 Score=18.51 Aligned_cols=17 Identities=41% Similarity=0.651 Sum_probs=14.1
Q ss_pred HCCCCHHHHHHHHHHHH
Q ss_conf 16763589999999999
Q gi|254781170|r 346 IGWMHNRLRMITASFLV 362 (483)
Q Consensus 346 tG~mhnr~Rm~vaSfl~ 362 (483)
.||||-|||.=|++|+-
T Consensus 215 KaymHsRMR~Rv~~flk 231 (242)
T pfam04045 215 KAYMHSRMRNRVAEFLK 231 (242)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999
No 35
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=46.36 E-value=21 Score=15.84 Aligned_cols=37 Identities=5% Similarity=-0.124 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHHCC
Q ss_conf 50899999999870976142100111001100102688875200
Q gi|254781170|r 88 DDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRV 131 (483)
Q Consensus 88 g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~~~ 131 (483)
.+.++...++....+|.-|.+ |.+ -|..+...++.+.
T Consensus 129 ~~~i~~~k~lL~~~Gi~~i~A-----p~E--Aeaqca~L~k~g~ 165 (338)
T TIGR03674 129 SEIVESSKKLLDLMGIPYVQA-----PSE--GEAQAAYMAKKGD 165 (338)
T ss_pred HHHHHHHHHHHHHCCCCEEEC-----CHH--HHHHHHHHHHCCC
T ss_conf 999999999999769876856-----727--9999999997497
No 36
>KOG2826 consensus
Probab=44.80 E-value=9.2 Score=18.13 Aligned_cols=17 Identities=41% Similarity=0.716 Sum_probs=13.6
Q ss_pred HCCCCHHHHHHHHHHHH
Q ss_conf 16763589999999999
Q gi|254781170|r 346 IGWMHNRLRMITASFLV 362 (483)
Q Consensus 346 tG~mhnr~Rm~vaSfl~ 362 (483)
-.|||-|||.-+++|+-
T Consensus 260 KaYmHsRMR~k~~dFlK 276 (301)
T KOG2826 260 KAYMHSRMRAKTSDFLK 276 (301)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999998876778999
No 37
>TIGR01426 MGT glycosyltransferase, MGT family; InterPro: IPR006326 These sequences belong to the MGT (macroside glycosyltransferase) subfamily of the UDP-glucuronosyltransferase family. Members include a number of glucosyl transferases for macrolide antibiotic inactivation, but also include transferases of glucose-related sugars for macrolide antibiotic production. ; GO: 0016758 transferase activity transferring hexosyl groups, 0016999 antibiotic metabolic process.
Probab=44.32 E-value=12 Score=17.45 Aligned_cols=42 Identities=24% Similarity=0.563 Sum_probs=30.3
Q ss_pred CCCCCCEEEEC--CCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHH
Q ss_conf 74561002012--789847022046458988724899783300824327997780
Q gi|254781170|r 388 NNGGWQWAAST--GNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYI 440 (483)
Q Consensus 388 n~~~wq~~a~~--G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~i 440 (483)
+-.+|+-+-++ ++|+.. ++|+ |.---||+|||.|.=++-.-.
T Consensus 288 ~~~GW~vV~~~g~~vDp~~----L~~~-------P~Nv~VR~~VPq~evL~~A~l 331 (429)
T TIGR01426 288 DLPGWHVVLSVGKGVDPAD----LGEL-------PKNVEVRRWVPQLEVLEKADL 331 (429)
T ss_pred CCCCCEEEEEECCCCCHHH----HCCC-------CCCEEEECCCCHHHHHHHHHH
T ss_conf 9987079997267026466----1679-------887788546562778988888
No 38
>TIGR01309 L30P_arch ribosomal protein L30P; InterPro: IPR005997 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L30 is one of the proteins from the large ribosomal subunit. L30 belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacteria and archaea L30, yeast mitochondrial L33, and Drosophila, slime mould, fungal and mammalian L7 ribosomal proteins This model describes archaeal 50S ribosomal protein L30. These proteins share similarity to the longer eukaryotic 60S ribosomal protein L7 and to the much shorter (~60 residue) bacterial 50S ribosomal protein L30. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=43.84 E-value=17 Score=16.36 Aligned_cols=53 Identities=13% Similarity=0.102 Sum_probs=33.4
Q ss_pred CCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCC-CC---HHHHHHHHHH
Q ss_conf 544611114648799999999998643111234772001023-20---2468887888
Q gi|254781170|r 243 SQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNE-LI---WREFYRHLMA 296 (483)
Q Consensus 243 SrLSPyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~e-L~---WRef~~~~~~ 296 (483)
-+-++|.+||.|+....-.=+.. ..+.......=++.|+.| +. =.||+..+..
T Consensus 46 ~kV~dYvTwGEid~~tL~~Li~~-Rgr~~~G~~~vtD~~v~E~t~~~~~~elA~al~~ 102 (160)
T TIGR01309 46 QKVKDYVTWGEIDEDTLELLIRK-RGRTLKGDKKVTDEYVKEVTGYESVDELAKALVE 102 (160)
T ss_pred CCCCCEEEECCCCHHHHHHHHHH-CCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHH
T ss_conf 10366545357597999999986-2887558986788887653288888899999874
No 39
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=41.45 E-value=25 Score=15.36 Aligned_cols=95 Identities=18% Similarity=0.157 Sum_probs=58.7
Q ss_pred CHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCC-CCCHHHHHHHHHHHC
Q ss_conf 7899999995798299999738378478889989999999999999999997598099996575-350899999999870
Q gi|254781170|r 23 NKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSN-FDDSIEWLDSYCLQQ 101 (483)
Q Consensus 23 N~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~-~g~~~~~L~~l~~~~ 101 (483)
+.||+.|.+.+- .|..+.+.-|...+. +-|-.-.+.-....-+..|+++....... .+.-++.|.++....
T Consensus 14 ~~Al~~a~~~G~-eV~~Ll~~~p~~~dS-------~m~H~~n~~~~~~~Ae~~gi~l~~~~~~g~~e~eve~L~~~l~~l 85 (223)
T COG2102 14 FYALYLALEEGH-EVVYLLTVKPENGDS-------YMFHTPNLELAELQAEAMGIPLVTFDTSGEEEREVEELKEALRRL 85 (223)
T ss_pred HHHHHHHHHCCC-EEEEEEEEECCCCCE-------EEEECCCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHC
T ss_conf 999999997598-368999981599870-------442222567999998744883599834763055699999999737
Q ss_pred CCCCEEEECCCCCHHHHCCHHHHHHHH
Q ss_conf 976142100111001100102688875
Q gi|254781170|r 102 RVTKLFYNRQYEINEVRRDKLLEKRLQ 128 (483)
Q Consensus 102 ~i~~v~~n~~~~~~~~~rd~~i~~~l~ 128 (483)
++..|..-..+.-+.+.| ++..|.
T Consensus 86 ~~d~iv~GaI~s~yqk~r---ve~lc~ 109 (223)
T COG2102 86 KVDGIVAGAIASEYQKER---VERLCE 109 (223)
T ss_pred CCCEEEECHHHHHHHHHH---HHHHHH
T ss_conf 633799734330999999---999999
No 40
>pfam10624 TraS Plasmid conjugative transfer entry exclusion protein TraS. Entry exclusion (Eex) is a process which prevents redundant transfer of DNA between donor cells. TraS is a protein involved in Eex. It blocks redundant conjugative DNA synthesis and transport between donor cells, and it is suggested that TraS interferes with a signalling pathway that is required to trigger DNA transfer. TraS on the recipient cell is known to form an interaction with TraG on the donor cell.
Probab=40.87 E-value=10 Score=17.83 Aligned_cols=11 Identities=18% Similarity=0.304 Sum_probs=5.3
Q ss_pred CCCCHHHHHHH
Q ss_conf 64879999999
Q gi|254781170|r 252 GVLSPRQCWNR 262 (483)
Q Consensus 252 G~IS~R~v~~~ 262 (483)
||||+|+-.+.
T Consensus 98 gcisikew~q~ 108 (164)
T pfam10624 98 GCISIKEWMKC 108 (164)
T ss_pred CCEEHHHHHHH
T ss_conf 42459999986
No 41
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=39.78 E-value=26 Score=15.20 Aligned_cols=94 Identities=19% Similarity=0.213 Sum_probs=49.4
Q ss_pred HHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECC-CCCCHHHHHHHHH---H
Q ss_conf 89999999579829999973837847888998999999999999999999759809999657-5350899999999---8
Q gi|254781170|r 24 KALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCS-NFDDSIEWLDSYC---L 99 (483)
Q Consensus 24 ~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~-~~g~~~~~L~~l~---~ 99 (483)
.||+.|.+.+. .|.++...-|.... +..|-.-.+.-++.+-+.+|++|+....+ ..++..+.+.+.. +
T Consensus 14 lAl~~a~~~g~-~v~~L~~~~~~~~~-------~~~~H~~~~~l~~~qAealgiPl~~~~~~~~~~~~~~~l~~~L~~~k 85 (194)
T cd01994 14 YALYRALEEGH-EVVALLNLTPEEGS-------SMMYHTVNHELLELQAEAMGIPLIRIEISGEEEDEVEDLKELLRKLK 85 (194)
T ss_pred HHHHHHHHCCC-EEEEEEEEECCCCC-------EEECCCCCHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 99999998699-25999999639988-------05250557899999999859966999668987179999999999999
Q ss_pred HCCCCCEEEECCCCCHHHHCCHHHHHHHH
Q ss_conf 70976142100111001100102688875
Q gi|254781170|r 100 QQRVTKLFYNRQYEINEVRRDKLLEKRLQ 128 (483)
Q Consensus 100 ~~~i~~v~~n~~~~~~~~~rd~~i~~~l~ 128 (483)
+.+|+.|.+-.-..-+.+.| +++.|.
T Consensus 86 ~~gi~~vv~GdI~s~~qr~~---~e~~c~ 111 (194)
T cd01994 86 EEGVDAVVFGAILSEYQRTR---VERVCE 111 (194)
T ss_pred HCCCCEEEECCCCCHHHHHH---HHHHHH
T ss_conf 75995999996332889999---999999
No 42
>PTZ00092 aconitate hydratase; Provisional
Probab=39.73 E-value=20 Score=15.91 Aligned_cols=10 Identities=50% Similarity=1.198 Sum_probs=5.1
Q ss_pred HCCCCCEEHC
Q ss_conf 2489978330
Q gi|254781170|r 418 FDPQGTFIRH 427 (483)
Q Consensus 418 ~Dp~g~~ir~ 427 (483)
+||+..||++
T Consensus 634 Wd~~STyI~~ 643 (887)
T PTZ00092 634 WDPKSTYIHH 643 (887)
T ss_pred CCCCCCEEEC
T ss_conf 8987644427
No 43
>TIGR00701 TIGR00701 conserved hypothetical protein TIGR00701; InterPro: IPR014351 There is currently no experimental data for members of this entry or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments). There is an indirect indication of a link between this protein and the function or assembly of cytochromes: in Escherichia coli, strains producing related proteins not included in this entry turn pink, perhaps because of an excess of accumulated haems ..
Probab=36.51 E-value=26 Score=15.29 Aligned_cols=47 Identities=19% Similarity=0.465 Sum_probs=26.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 99716763589999999999841047002233477664133111474561002012789847022046
Q gi|254781170|r 343 LNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFN 410 (483)
Q Consensus 343 L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~~~~~Ri~n 410 (483)
++.|||+|..| ..|+=-+.+|-. .++..=|.+-+-| ||.+ -.+|++|
T Consensus 82 ~ksgGWl~~Kl-~~V~lLl~yHfy---------c~r~~k~lakg~~----~~s~-------~fyR~~N 128 (151)
T TIGR00701 82 LKSGGWLHIKL-ALVVLLLIYHFY---------CARVMKDLAKGKS----RRSK-------KFYRVLN 128 (151)
T ss_pred HCCCCHHHHHH-HHHHHHHHHHHH---------HHHHHHHHHCCCC----CCCC-------HHHHHHH
T ss_conf 00245599999-999999999999---------9999999743865----2132-------1301243
No 44
>KOG3636 consensus
Probab=35.38 E-value=24 Score=15.49 Aligned_cols=34 Identities=38% Similarity=0.619 Sum_probs=24.1
Q ss_pred CHHHHHHHHHHHHHH-HCCCHHHHH-----HHHHHHHHCC
Q ss_conf 358999999999984-104700223-----3477664133
Q gi|254781170|r 350 HNRLRMITASFLVKD-LLVDWRIGE-----EYFMSQLLDG 383 (483)
Q Consensus 350 hnr~Rm~vaSfl~~~-L~idWr~g~-----~~f~~~llD~ 383 (483)
-|+|-|++|+||-|+ +.+.---|. .||+.+..|.
T Consensus 398 D~YmnMviA~FlQKnk~yVS~~~GGy~~lh~~~~d~~~Dc 437 (669)
T KOG3636 398 DNYMNMVIAMFLQKNKLYVSFVQGGYKKLHDYFGDQMADC 437 (669)
T ss_pred HHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCC
T ss_conf 7899999999986486699874243899999753430257
No 45
>TIGR00464 gltX_bact glutamyl-tRNA synthetase; InterPro: IPR004527 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of E. coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure . ; GO: 0000166 nucleotide binding, 0004818 glutamate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006424 glutamyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=32.78 E-value=33 Score=14.59 Aligned_cols=29 Identities=17% Similarity=0.473 Sum_probs=19.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf 999999997167635899999999998410470022
Q gi|254781170|r 337 DAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIG 372 (483)
Q Consensus 337 DA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g 372 (483)
.-...|+++.||+. -.++.||+ .+-|..+
T Consensus 274 ~~si~q~~~~GyLP----EAl~Nyl~---lLGW~~~ 302 (513)
T TIGR00464 274 ATSIEQFKEQGYLP----EALINYLA---LLGWSPP 302 (513)
T ss_pred HHHHHHHHHCCCCH----HHHHHHHH---HHCCCCC
T ss_conf 57689998668877----89999999---8468965
No 46
>PRK09613 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=31.89 E-value=24 Score=15.45 Aligned_cols=22 Identities=36% Similarity=0.493 Sum_probs=11.5
Q ss_pred HHCCCCCCHHHHHHHHHHHHCCCCHHH
Q ss_conf 722788868899999999716763589
Q gi|254781170|r 327 KQGYTGFPIIDAAMRQLNTIGWMHNRL 353 (483)
Q Consensus 327 ~~G~TG~PlVDA~MR~L~~tG~mhnr~ 353 (483)
..|+|| |-=| +|..+|.++|-+
T Consensus 390 R~GRTG----~~FM-~lak~g~I~~~C 411 (471)
T PRK09613 390 RKGRTG----DRFM-SLAKSGQIKNFC 411 (471)
T ss_pred CCCCCH----HHHH-HHHHCCCCCCCC
T ss_conf 689857----8899-862043623665
No 47
>PRK10682 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional
Probab=31.72 E-value=35 Score=14.39 Aligned_cols=78 Identities=15% Similarity=0.165 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHHHHH
Q ss_conf 02233477664133111474561002012789847022046458988724899783300824327997780495540131
Q gi|254781170|r 370 RIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDK 449 (483)
Q Consensus 370 r~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~~~~ 449 (483)
...|.-|...++|=|.|.-..+. ..--+|.+-+..+=| ||+++-|.-+. | .
T Consensus 289 ~~~A~~FInf~l~Pe~aa~~~~~-------------~~y~~~n~~A~~~l~---------~e~~~~~~i~p--~-----~ 339 (370)
T PRK10682 289 KDEAYQFLNYLLRPDVIAHISDH-------------VFYANANKAATPLVS---------AEVRDNPGIYP--P-----A 339 (370)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHH-------------HCCCCHHHHHHHHCC---------HHHHHCCCCCC--C-----H
T ss_conf 69999999985097999999986-------------478875389886189---------98861987689--9-----9
Q ss_pred CCCCCCCCCCCCCHHH--HHHHHHHHHHH
Q ss_conf 2578999976318999--99999999999
Q gi|254781170|r 450 NDLSLNYPLPIVDHKK--ACHHTLNQYYA 476 (483)
Q Consensus 450 ~~~~~~YP~pivd~~~--~~~~a~~~~~~ 476 (483)
..+.+-++.+.++-+. .+.+...++|.
T Consensus 340 ~~~~~~~~~~~~~~~~~~~~~~~W~~iKs 368 (370)
T PRK10682 340 DVRAKLFTLKVQDPKIDRVRTRAWTKVKS 368 (370)
T ss_pred HHHHCCEECCCCCHHHHHHHHHHHHHHHC
T ss_conf 99943813368998999999999998654
No 48
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=30.76 E-value=37 Score=14.29 Aligned_cols=70 Identities=11% Similarity=0.148 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHH-CCCCEEC
Q ss_conf 999999999999975980999965753508999999998709761421001110011001026888752-0000002
Q gi|254781170|r 61 IYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH-RVICKSF 136 (483)
Q Consensus 61 l~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~-~~~~~~~ 136 (483)
|-+=|..+.+++.++|+..++-. +-.|+.+++.+++.+.++++|+..+.-..+++.- .+.|+. ++.+++.
T Consensus 63 Ld~~l~~~~~~v~~~Gg~vy~A~--~aedA~~ii~~iv~~k~~k~vVKsKSmvseEIgl----n~~Le~~G~ev~ET 133 (459)
T COG1139 63 LDEYLEQLEENVTRNGGHVYFAK--DAEDAREIIGEIVGEKNGKKVVKSKSMVSEEIGL----NHYLEEKGIEVWET 133 (459)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEC--CHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHH----HHHHHHCCCEEEEC
T ss_conf 89999999999997198799837--8899999999997541675788742315877526----89998749847872
No 49
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=29.90 E-value=38 Score=14.19 Aligned_cols=11 Identities=18% Similarity=-0.133 Sum_probs=3.8
Q ss_pred CCCCCHHHCCC
Q ss_conf 65446111146
Q gi|254781170|r 242 TSQLSPYLSIG 252 (483)
Q Consensus 242 tSrLSPyL~~G 252 (483)
.|+=+-|-+|+
T Consensus 40 vS~G~v~~yF~ 50 (189)
T TIGR03384 40 VSSGIISHYFG 50 (189)
T ss_pred CCHHHHHHHCC
T ss_conf 99999999838
No 50
>PRK11622 putative ABC transporter solute-binding protein; Provisional
Probab=29.85 E-value=31 Score=14.76 Aligned_cols=139 Identities=17% Similarity=0.214 Sum_probs=64.6
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCC---
Q ss_conf 99872278886889999999971676358999999999984104700223347766413311147456100201278---
Q gi|254781170|r 324 QAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGN--- 400 (483)
Q Consensus 324 ~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~--- 400 (483)
-.|++|+| ||-=-+.|++|...|=+..-|--.-+........---....+-| + ++-+ ..+|-.+.|=--+
T Consensus 242 ~LWr~G~~-yP~~~~~l~~L~adGEi~~~~sfnp~~a~~~I~~G~lP~t~r~~----~-~~~G-tigN~hflAIP~NA~~ 314 (401)
T PRK11622 242 YLWRKGKT-FPASPAELDQLLADGELDLAFTFNPNEAQAAIANGELPASTRSF----A-FSDG-TIGNTHFVAIPFNANA 314 (401)
T ss_pred HHHHCCCC-CCCCHHHHHHHHHCCCEEEEEECCHHHHHHHHHCCCCCCCEEEE----E-CCCC-CCCCCCCEEEECCCCC
T ss_conf 88844012-68999999999847987788403877788898669999740267----4-2698-2167650772079998
Q ss_pred -----CCCCCCCCCCHHHHHHHHCCC--CCEEHCCCHHHHCCCHHHHCC------HHHHHHHCCCC-CCCCCCCCCHHHH
Q ss_conf -----984702204645898872489--978330082432799778049------55401312578-9999763189999
Q gi|254781170|r 401 -----DSVPYFRIFNPTIQGKRFDPQ--GTFIRHWLPELNNVPTQYIHA------PHSWLDKNDLS-LNYPLPIVDHKKA 466 (483)
Q Consensus 401 -----d~~~~~Ri~np~~q~~~~Dp~--g~~ir~wvPeL~~~p~~~ih~------p~~~~~~~~~~-~~YP~pivd~~~~ 466 (483)
-.+|+ +.+|..|.+|+||+ |++- |=.+..++.+.--. ....+...+++ .--|+| ..+
T Consensus 315 kagA~VvaNf--LLSPEAQ~~K~~p~~WGd~t---VLd~~kL~~~~r~~F~~l~~g~atl~~~~L~~~~lpEp----h~s 385 (401)
T PRK11622 315 KAGAKVVANF--LLSPEAQLRKADPAVWGDPS---VLDPQKLPEEQRATFAALKLGAATLPPEELPFPALPEP----HAS 385 (401)
T ss_pred HHHHHHHHHH--HCCHHHHHHHCCCCCCCCCC---CCCHHHCCHHHHHHHHCCCCCCCCCCHHHHCCCCCCCC----CHH
T ss_conf 7789999999--63999999753864248854---11645389999998855566778889567333247898----869
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999996
Q gi|254781170|r 467 CHHTLNQYYAAK 478 (483)
Q Consensus 467 ~~~a~~~~~~~~ 478 (483)
--.++++-|..|
T Consensus 386 w~~~iE~~W~~r 397 (401)
T PRK11622 386 WVEALEKEWQRR 397 (401)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999997
No 51
>PTZ00217 flap endonuclease-1; Provisional
Probab=29.51 E-value=39 Score=14.15 Aligned_cols=85 Identities=5% Similarity=-0.060 Sum_probs=35.8
Q ss_pred CEEEEEEECHHHHCCC-CCCHHHHHHHHHHHHHHHHHHH--------HCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf 2999997383784788-8998999999999999999999--------759809999657535089999999987097614
Q gi|254781170|r 36 KVIAVFIATPEQWRQH-GISARQSHFIYASLLQVQKSLS--------QKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKL 106 (483)
Q Consensus 36 ~vlpvyi~dp~~~~~~-~~~~~~~~Fl~esL~~L~~~L~--------~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~v 106 (483)
.|.||||||..-.... ..-..|..=-.++...+++.+. ++-.+.+-. ..+.++.+.++....+|.-|
T Consensus 80 gIkPVfVFDGkpp~~K~~tl~kRr~~R~eA~~~~~~a~e~gd~e~a~k~~~r~v~v----T~e~~~~~k~LL~~mGIpyI 155 (394)
T PTZ00217 80 GIKPIYVFDGKPPELKSGELEKRRQRREEAEAELEKAKEEGDDEQMKKQSKRTVRV----TRKQNEEAKKLLRLMGIPVI 155 (394)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC----CHHHHHHHHHHHHHCCCCEE
T ss_conf 99799997899943558899999999999999999998758999999987543538----89999999999997699768
Q ss_pred EEECCCCCHHHHCCHHHHHHHHHCC
Q ss_conf 2100111001100102688875200
Q gi|254781170|r 107 FYNRQYEINEVRRDKLLEKRLQHRV 131 (483)
Q Consensus 107 ~~n~~~~~~~~~rd~~i~~~l~~~~ 131 (483)
.+ |++ -|..+...++.+.
T Consensus 156 ~A-----P~E--AEaqcA~L~~~g~ 173 (394)
T PTZ00217 156 EA-----PSE--AEAQCAELVKKGK 173 (394)
T ss_pred EC-----CCH--HHHHHHHHHHCCC
T ss_conf 65-----805--9999999996696
No 52
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=27.49 E-value=30 Score=14.82 Aligned_cols=25 Identities=28% Similarity=0.331 Sum_probs=17.9
Q ss_pred CHHHHHHHHHCC----CCC-CHHHHHHHHH
Q ss_conf 046789987227----888-6889999999
Q gi|254781170|r 319 DSHLLQAWKQGY----TGF-PIIDAAMRQL 343 (483)
Q Consensus 319 ~~~~~~aW~~G~----TG~-PlVDA~MR~L 343 (483)
+++....+-.|. ||| |||||.||--
T Consensus 120 t~~eI~~aL~GnLCRCtgY~~Iv~Av~~~a 149 (151)
T TIGR03198 120 SDEDMEEGLSGNLCRCTGYGGIIRSACRIR 149 (151)
T ss_pred CHHHHHHHHCCCCCCCCCCHHHHHHHHHHH
T ss_conf 999999986677333799879999999984
No 53
>PRK10490 sensor protein KdpD; Provisional
Probab=25.85 E-value=45 Score=13.74 Aligned_cols=97 Identities=14% Similarity=0.189 Sum_probs=57.8
Q ss_pred CCHHHHH-H---HHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHH
Q ss_conf 7789999-9---99579829999973837847888998999999999999999999759809999657535089999999
Q gi|254781170|r 22 DNKALYA-A---CHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSY 97 (483)
Q Consensus 22 DN~aL~~-A---~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g~~~~~L~~l 97 (483)
.+..|.. | +..-+++.+.|||-.|... ..+.....-+...+ .|.+ ++|...+...| +|..+.|.++
T Consensus 262 ~~~~lir~~~r~a~~~~~~~~~~~v~~~~~~---~~~~~~~~~~~~~~-~LAe---~LGa~v~~l~G---~dva~~il~~ 331 (895)
T PRK10490 262 GSEKLVRTAARLAARLGSVWHAVYVETPRLH---RLPEKKRRAILSAL-RLAQ---ELGAETATLSD---PAEEKAVVRY 331 (895)
T ss_pred CCHHHHHHHHHHHHHCCCCEEEEEEECCCCC---CCCHHHHHHHHHHH-HHHH---HHCCEEEEEEC---CCHHHHHHHH
T ss_conf 7469999999999847998699999644445---79877899999999-9999---81998999837---9889999999
Q ss_pred HHHCCCCCEEEECCCCCHHHHCCHHHHHHHH
Q ss_conf 9870976142100111001100102688875
Q gi|254781170|r 98 CLQQRVTKLFYNRQYEINEVRRDKLLEKRLQ 128 (483)
Q Consensus 98 ~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~ 128 (483)
++..++++|+.-+........+.....+..+
T Consensus 332 Ar~~nvT~IVlGrs~~rrw~~r~sl~drLi~ 362 (895)
T PRK10490 332 AREHNLGKIIIGRPASRRWWRRETFADRLAR 362 (895)
T ss_pred HHHCCCCEEEECCCCCCCCCCCCCHHHHHHH
T ss_conf 9983999899888788750337889999987
No 54
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=24.76 E-value=24 Score=15.47 Aligned_cols=19 Identities=16% Similarity=0.429 Sum_probs=12.1
Q ss_pred HHHHHH---HHHCCCCHHHHHH
Q ss_conf 999999---9716763589999
Q gi|254781170|r 338 AAMRQL---NTIGWMHNRLRMI 356 (483)
Q Consensus 338 A~MR~L---~~tG~mhnr~Rm~ 356 (483)
+.||-- ..|||+.+|.|--
T Consensus 471 c~LRr~L~~~~~~YL~~RiRrY 492 (664)
T TIGR02062 471 CKLRRELEAQETDYLDSRIRRY 492 (664)
T ss_pred HHHHHHHCCCCCCHHHHHHHHH
T ss_conf 8887753027866134446664
No 55
>TIGR01890 N-Ac-Glu-synth amino-acid N-acetyltransferase; InterPro: IPR010167 This entry represents a clade of amino-acid N-acetyltransferases, or N-acetylglutamate synthase, which is the product of the argA gene and the first enzyme in arginine biosynthesis. This enzyme displays more diversity between bacteria, fungi and mammals than other enzymes in arginine metabolism, and N-acetylglutamate itself can have different roles in different taxonomic groups: in prokaryotes, lower eukaryotes and plants it is the first intermediate in arginine biosynthesis, while in vertebrates it is an allosteric cofactor for the first enzyme in the urea cycle . In bacteria, arginine can regulate ornithine biosynthesis via a feedback inhibition mechanism . This enzyme may also act on aspartate.; GO: 0004042 amino-acid N-acetyltransferase activity, 0006526 arginine biosynthetic process, 0005737 cytoplasm.
Probab=24.37 E-value=34 Score=14.49 Aligned_cols=18 Identities=28% Similarity=0.375 Sum_probs=11.2
Q ss_pred ECCCCCCCCCHHHHHHHH
Q ss_conf 358675567789999999
Q gi|254781170|r 14 LRNDLRITDNKALYAACH 31 (483)
Q Consensus 14 fRrDLRl~DN~aL~~A~~ 31 (483)
|.|-+|++||.+|..|.+
T Consensus 74 Y~~G~RvTD~asLe~~~~ 91 (439)
T TIGR01890 74 YHRGLRVTDEASLELVKQ 91 (439)
T ss_pred CCCCEEECCHHHHHHHHH
T ss_conf 032257135656778999
No 56
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=24.35 E-value=48 Score=13.56 Aligned_cols=14 Identities=14% Similarity=-0.031 Sum_probs=6.2
Q ss_pred HHCCCCHHHHHHHH
Q ss_conf 71676358999999
Q gi|254781170|r 345 TIGWMHNRLRMITA 358 (483)
Q Consensus 345 ~tG~mhnr~Rm~va 358 (483)
+.+==|--.++++.
T Consensus 444 E~~S~HPlA~AIv~ 457 (713)
T COG2217 444 EQHSEHPLAKAIVK 457 (713)
T ss_pred HHHCCCHHHHHHHH
T ss_conf 73088958999999
No 57
>KOG0452 consensus
Probab=24.07 E-value=39 Score=14.10 Aligned_cols=12 Identities=17% Similarity=0.418 Sum_probs=5.8
Q ss_pred HHHHHHHHHCCC
Q ss_conf 999999640079
Q gi|254781170|r 472 NQYYAAKKQSLL 483 (483)
Q Consensus 472 ~~~~~~~k~~~~ 483 (483)
+-|+.+-+++||
T Consensus 801 eS~ErIHrsnLv 812 (892)
T KOG0452 801 ESYERIHRSNLV 812 (892)
T ss_pred HHHHHHHHHCCC
T ss_conf 889888763544
No 58
>pfam05889 SLA_LP_auto_ag Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). This family consists of several eukaryotic and archaeal proteins which are related to the human soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway. Some archaeal members are annotated as being pyridoxal phosphate-dependent enzymes.
Probab=23.80 E-value=49 Score=13.50 Aligned_cols=120 Identities=15% Similarity=0.313 Sum_probs=69.4
Q ss_pred EEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCE--EEEEECC--
Q ss_conf 688835867556778999999957982999997383784788899899999999999999999975980--9999657--
Q gi|254781170|r 10 HLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIV--FQYHQCS-- 85 (483)
Q Consensus 10 ~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~--L~v~~~~-- 85 (483)
-|+|=| +.-..++ .|+..++ +.|+.| ++...+ + .+.--+.++++.++++|.. +-|+..+
T Consensus 103 yViw~R----iDqKSc~-Kai~~AG--l~p~vV-e~~~~~--d-------~l~Td~~~ie~~i~~~g~~~ilcVlsTTSc 165 (389)
T pfam05889 103 YVIWPR----IDQKSSI-KAAERAG--FEPRLV-ETVLDG--D-------YLITDVNDVETIIEEKGEEVILAVLSTTSC 165 (389)
T ss_pred EEEEEC----CCCCCHH-HHHHHCC--CEEEEE-EEEECC--C-------EEECCHHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf 899863----5552268-9999769--714887-525228--8-------243589999999998387766899844665
Q ss_pred ---CCCCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHH---CCCCEECCCCCCCCCCCC
Q ss_conf ---53508999999998709761421001110011001026888752---000000223434555760
Q gi|254781170|r 86 ---NFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH---RVICKSFDDSVLLPPGSI 147 (483)
Q Consensus 86 ---~~g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~---~~~~~~~~~~~l~~p~~i 147 (483)
+..|-+..+.++|++++|-+|+-| .|+.....--+.|.+.... ...+++.+-++++|.+.-
T Consensus 166 FaPR~pD~v~~IAklC~~~~IpHvVNn-AYGlQ~~~~~~~i~~a~r~GRVDa~VQStDKNflVPVGGa 232 (389)
T pfam05889 166 FAPRSPDNVKEIAKICAEYDVPHLVNG-AYGIQSEETIRLIAAAHECGRVDAVVQSLDKNFIVPVGGA 232 (389)
T ss_pred CCCCCCCCHHHHHHHHHHCCCCEEECC-HHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEECCCE
T ss_conf 699996679999999997499747843-0366179999999999863882189970686625534874
No 59
>PRK02249 DNA primase large subunit; Validated
Probab=23.16 E-value=50 Score=13.42 Aligned_cols=64 Identities=22% Similarity=0.163 Sum_probs=41.5
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECC
Q ss_conf 688999999997167635899999999998410470022334776641331114745610020127
Q gi|254781170|r 334 PIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTG 399 (483)
Q Consensus 334 PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G 399 (483)
|=+-++...|.+-.=+++-+|..+||||. +++++=..-...|. .-=|||...---|-+-++|.|
T Consensus 223 PCmk~~i~~l~~G~Nl~H~~Rf~Lasfl~-~iG~~~d~i~~lf~-~aPDf~e~~t~YQv~hi~g~~ 286 (333)
T PRK02249 223 PCMKALLSALQAGENLPHTARFAITSFLH-NIGMDVDEIVELFR-NAPDFDEEITRYQVEHIAGEG 286 (333)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHH-HCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHCCCC
T ss_conf 07999999986699877178999999999-76998899999984-199866024678887622788
No 60
>pfam10406 TAF8_C Transcription factor TFIID complex subunit 8 C-term. This is the C-terminal, Delta, part of the TAF8 protein. The N-terminal is generally the histone fold domain, Bromo_TP (pfam07524). TAF8 is one of the key subunits of the transcription factor for pol II, TFIID. TAF8 is one of the several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery.
Probab=23.08 E-value=50 Score=13.41 Aligned_cols=42 Identities=24% Similarity=0.564 Sum_probs=27.9
Q ss_pred CEEHCCCHHHHCCCHHHHCCHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 783300824327997780495540131257899997631899999999999999
Q gi|254781170|r 423 TFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYA 476 (483)
Q Consensus 423 ~~ir~wvPeL~~~p~~~ih~p~~~~~~~~~~~~YP~pivd~~~~~~~a~~~~~~ 476 (483)
.||=.|+|++=+ |-.|++.| -|..|+-|.+.-|+++.+.=+.
T Consensus 1 syIP~~lP~fP~-~HTY~~TP-----------~~~~~~td~~~iRe~~a~q~r~ 42 (51)
T pfam10406 1 SYIPSWLPDFPP-DHTYKKTP-----------VYTEPVTDPRKIREKLVEESRL 42 (51)
T ss_pred CCCCCCCCCCCC-CCCCCCCC-----------CCCCCCCCHHHHHHHHHHHHHH
T ss_conf 988655899989-75322478-----------6678889889999999999999
No 61
>TIGR00071 hisT_truA tRNA pseudouridine synthase A; InterPro: IPR001406 Transfer RNA-pseudouridine synthetase contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis. It is involved in the formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer-RNAs. Pseudouridine is the most abundant modified nucleoside found in all cellular RNAs.; GO: 0000049 tRNA binding, 0016439 tRNA-pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0008033 tRNA processing.
Probab=22.80 E-value=51 Score=13.38 Aligned_cols=22 Identities=9% Similarity=0.261 Sum_probs=18.1
Q ss_pred HHHHHCCCCHHHHHHHHHHHHH
Q ss_conf 9997167635899999999998
Q gi|254781170|r 342 QLNTIGWMHNRLRMITASFLVK 363 (483)
Q Consensus 342 ~L~~tG~mhnr~Rm~vaSfl~~ 363 (483)
.+.-.|||+|-+|+||++.+--
T Consensus 272 ~I~G~~FL~~mVR~iV~~l~~~ 293 (326)
T TIGR00071 272 DIIGNSFLWHMVRKIVGALVLV 293 (326)
T ss_pred EEEECCCHHHHHHHHHHHHHHH
T ss_conf 9885430388899999999997
No 62
>pfam04858 TH1 TH1 protein. TH1 is a highly conserved but uncharacterized metazoan protein. No homologue has been identified in Caenorhabditis elegans. TH1 binds specifically to A-Raf kinase.
Probab=22.70 E-value=51 Score=13.36 Aligned_cols=22 Identities=27% Similarity=0.250 Sum_probs=13.6
Q ss_pred CCCCCCHHHCCCCCCHHHHHHH
Q ss_conf 6654461111464879999999
Q gi|254781170|r 241 GTSQLSPYLSIGVLSPRQCWNR 262 (483)
Q Consensus 241 ~tSrLSPyL~~G~IS~R~v~~~ 262 (483)
.|..|+--|.-|+++|-.|-.-
T Consensus 286 a~~al~smLs~~~lnp~Di~~L 307 (582)
T pfam04858 286 ACYALADMLSRGALNPADITVL 307 (582)
T ss_pred HHHHHHHHHCCCCCCHHHHHHH
T ss_conf 9999999864289986779999
No 63
>COG4168 SapB ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]
Probab=22.39 E-value=34 Score=14.53 Aligned_cols=21 Identities=19% Similarity=0.370 Sum_probs=7.9
Q ss_pred CCHHHHHHHHHHHHHCCCHHC
Q ss_conf 470022334776641331114
Q gi|254781170|r 367 VDWRIGEEYFMSQLLDGDLAS 387 (483)
Q Consensus 367 idWr~g~~~f~~~llD~d~~~ 387 (483)
..|--=.+|+-+-.-.-|.++
T Consensus 263 f~WPGiGRWLinAi~qqDy~s 283 (321)
T COG4168 263 FGWPGIGRWLINAIRQQDYAS 283 (321)
T ss_pred CCCCCHHHHHHHHHHHCCHHH
T ss_conf 289752599999987600676
No 64
>TIGR01316 gltA glutamate synthase (NADPH), homotetrameric; InterPro: IPR006004 One pathway for the assimilation of ammonia and glutamate biosynthesis involves homotetrameric glutamate synthase (1.4.1.13 from EC) which transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate . 2 L-glutamate + NADP^+ = L-glutamine + 2-oxoglutarate + NADPH + H^+. .
Probab=22.28 E-value=52 Score=13.31 Aligned_cols=45 Identities=13% Similarity=0.284 Sum_probs=28.5
Q ss_pred HHHHHHHH-HHHHHCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf 99999999-9999759809999657535089999999987097614210
Q gi|254781170|r 62 YASLLQVQ-KSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYN 109 (483)
Q Consensus 62 ~esL~~L~-~~L~~~g~~L~v~~~~~~g~~~~~L~~l~~~~~i~~v~~n 109 (483)
=.++.+-. +.|+++|+.+..-.. .|..++ |.+|.++|+.++||.-
T Consensus 191 pKei~~~E~k~LkklGv~fr~~~l--vGkt~T-L~eL~~~YGfDAVFIg 236 (462)
T TIGR01316 191 PKEIVETEVKKLKKLGVKFRTDYL--VGKTVT-LEELLEKYGFDAVFIG 236 (462)
T ss_pred CHHHHHHHHHHHHHCCEEEEECCE--ECCCHH-HHHHHHHCCCCEEEEE
T ss_conf 757889888876326637994437--505112-8888875197079995
No 65
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=21.57 E-value=54 Score=13.22 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=5.8
Q ss_pred HHHHHHCCCCHHH
Q ss_conf 9999716763589
Q gi|254781170|r 341 RQLNTIGWMHNRL 353 (483)
Q Consensus 341 R~L~~tG~mhnr~ 353 (483)
+.|..||-+..|-
T Consensus 268 ~~l~~~G~~~~~R 280 (333)
T TIGR00750 268 KFLTESGLLEEKR 280 (333)
T ss_pred HHHHHCCCHHHHH
T ss_conf 9998636067999
No 66
>COG5394 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.14 E-value=55 Score=13.16 Aligned_cols=35 Identities=20% Similarity=0.447 Sum_probs=19.9
Q ss_pred CCCCCCHHH-HHHHHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf 278886889-9999999716763589999999999841
Q gi|254781170|r 329 GYTGFPIID-AAMRQLNTIGWMHNRLRMITASFLVKDL 365 (483)
Q Consensus 329 G~TG~PlVD-A~MR~L~~tG~mhnr~Rm~vaSfl~~~L 365 (483)
.+||-|+.- +-.|||. +|--|.|-|+|-|||-+.+
T Consensus 69 ~k~G~~llpi~fLrQlI--~fYGdqMQ~~vpsyLE~sm 104 (193)
T COG5394 69 NKGGQNLLPISFLRQLI--SFYGDQMQMVVPSYLEHSM 104 (193)
T ss_pred CCCCCCCCCHHHHHHHH--HHHHHHHHHHHHHHHHHHH
T ss_conf 05897146399999999--9986889988799999999
No 67
>TIGR00308 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs . The enzyme is found in both eukaryotes and archaea .; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing.
Probab=20.96 E-value=56 Score=13.14 Aligned_cols=79 Identities=16% Similarity=0.259 Sum_probs=41.6
Q ss_pred CCCCCCCHHHHHHHHHHCCCC-CCCCCCCC-CCCCCCC-CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 864432101479988631566-32212455-4456776-6755575323-476434554688876433322111111101
Q gi|254781170|r 152 LQMYKVYTPFRKALIQNLVQA-DLRSLPVP-AIRLTGP-VTPSNIPRFF-DYPFQAIDPMFPIGEQNALHILRKFCKEKV 227 (483)
Q Consensus 152 ~~~~~vftpf~k~~~~~~~~~-~~~~~p~~-~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~gGe~~A~~~L~~Fl~~~l 227 (483)
.+||.+=+||.-...+..... .+...... ...+.+. .....+.... ..+. .-.-.++.|++.|-.|+...+
T Consensus 176 iDPFGspAPFvd~A~~~~~~~NglL~vTATDta~LcG~G~~~~CL~kY~GA~~l-----~~~~~HE~aLR~l~gf~~~~a 250 (462)
T TIGR00308 176 IDPFGSPAPFVDSAIRASAKRNGLLLVTATDTAALCGSGYKKSCLRKYGGAFPL-----KTESCHEVALRLLVGFVVREA 250 (462)
T ss_pred ECCCCCCCCHHHHHHHHHHHCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCC-----CCCCCHHHHHHHHHHHHHHHH
T ss_conf 478779741589999999746860440667899862788862124543013454-----676430689999999999888
Q ss_pred CHHHHCCC
Q ss_conf 10120268
Q gi|254781170|r 228 YYYVEQRD 235 (483)
Q Consensus 228 ~~Y~~~Rn 235 (483)
..|+++-.
T Consensus 251 akY~kA~~ 258 (462)
T TIGR00308 251 AKYEKALE 258 (462)
T ss_pred HHHHHHHH
T ss_conf 75677644
No 68
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621; InterPro: IPR006508 These sequences represent a clade within the pseudouridine synthase superfamily. The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences in this family are most closely related to RluA ; only Neisseria does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity..
Probab=20.89 E-value=31 Score=14.76 Aligned_cols=15 Identities=27% Similarity=0.295 Sum_probs=7.4
Q ss_pred HHHHHHHCCCCCEEE
Q ss_conf 999998709761421
Q gi|254781170|r 94 LDSYCLQQRVTKLFY 108 (483)
Q Consensus 94 L~~l~~~~~i~~v~~ 108 (483)
+..++.+.++.+||.
T Consensus 32 ~~~vA~Qlgv~~vwL 46 (222)
T TIGR01621 32 LREVAKQLGVEKVWL 46 (222)
T ss_pred HHHHHHHHCCCCEEE
T ss_conf 999999818980899
No 69
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=20.85 E-value=56 Score=13.12 Aligned_cols=24 Identities=29% Similarity=0.463 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 889999999971676358999999
Q gi|254781170|r 335 IIDAAMRQLNTIGWMHNRLRMITA 358 (483)
Q Consensus 335 lVDA~MR~L~~tG~mhnr~Rm~va 358 (483)
|+||+++.+.+.||-.-.||.+..
T Consensus 1 Il~aA~~l~~~~G~~~~s~~~Ia~ 24 (47)
T pfam00440 1 ILDAALELFAEKGYDATTVREIAK 24 (47)
T ss_pred CHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf 999999999986915077999999
No 70
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.75 E-value=50 Score=13.45 Aligned_cols=32 Identities=19% Similarity=0.369 Sum_probs=15.9
Q ss_pred CHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCC
Q ss_conf 0001046789987227888688999999997167
Q gi|254781170|r 315 EWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGW 348 (483)
Q Consensus 315 ~w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~ 348 (483)
+|-+|...+..= -|..- |-+.-.|-+|...||
T Consensus 317 p~fydl~~ias~-l~~s~-p~~~~vv~~L~~~G~ 348 (380)
T COG1867 317 PLFYDLHRIASK-LGLSA-PPLEEVVEALRSAGY 348 (380)
T ss_pred CEEEEHHHHHHH-HCCCC-CCHHHHHHHHHHCCC
T ss_conf 627778999998-57899-998999999985472
No 71
>cd04374 RhoGAP_Graf RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences cytoskeletal changes mediated by Rho proteins. Graf exhibits GAP activity toward RhoA and Cdc42, but only weakly activates Rac1. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=20.47 E-value=57 Score=13.07 Aligned_cols=17 Identities=12% Similarity=0.151 Sum_probs=11.2
Q ss_pred CHHHHHHHHHHHHHHHH
Q ss_conf 98999999999999999
Q gi|254781170|r 54 SARQSHFIYASLLQVQK 70 (483)
Q Consensus 54 ~~~~~~Fl~esL~~L~~ 70 (483)
++-...|+..|...+.+
T Consensus 25 ~~~~~~iV~kCI~~Ie~ 41 (203)
T cd04374 25 DDIGFKFVRKCIEAVET 41 (203)
T ss_pred CCCCCHHHHHHHHHHHH
T ss_conf 55371999999999998
No 72
>TIGR00597 rad10 DNA repair protein rad10; InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA.; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus.
Probab=20.36 E-value=34 Score=14.49 Aligned_cols=79 Identities=14% Similarity=0.160 Sum_probs=39.6
Q ss_pred CCCCCHHHHHH-------HHHCCCCEEEEEEECHHHHC---CCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC
Q ss_conf 55677899999-------99579829999973837847---888998999999999999999999759809999657535
Q gi|254781170|r 19 RITDNKALYAA-------CHNSDAKVIAVFIATPEQWR---QHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFD 88 (483)
Q Consensus 19 Rl~DN~aL~~A-------~~~~~~~vlpvyi~dp~~~~---~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~g 88 (483)
|=..||-|.+- ..+.+-.++|=|++-..... .-.+..=|..++.+=|..|.++...+ +-|++. +..
T Consensus 8 rQkgNPlL~hvrnvpW~y~sstGi~~ipd~vlg~g~c~LFLsL~YH~LhpdYI~~R~q~Lgkn~nlR-iLl~~V---Dv~ 83 (117)
T TIGR00597 8 RQKGNPLLKHVRNVPWEYVSSTGIDVIPDYVLGRGRCVLFLSLKYHKLHPDYISRRLQKLGKNFNLR-ILLVLV---DVK 83 (117)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEECCCEECCEEEEEEEECCCCCCCHHHHHHHHHHCCCCCCCE-EEEEEE---ECC
T ss_conf 7577876411034884100225421320313022033233200015636347876300302210044-778896---058
Q ss_pred CHHHHHHHHHHHC
Q ss_conf 0899999999870
Q gi|254781170|r 89 DSIEWLDSYCLQQ 101 (483)
Q Consensus 89 ~~~~~L~~l~~~~ 101 (483)
++.+.|.+++|-+
T Consensus 84 n~~~~l~el~K~c 96 (117)
T TIGR00597 84 NSQDALKELTKLC 96 (117)
T ss_pred CHHHHHHHHHHHH
T ss_conf 8588899999887
No 73
>pfam08471 Ribonuc_red_2_N Class II vitamin B12-dependent ribonucleotide reductase. This domain is found to the N-terminus of the ribonucleotide reductase barrel domain (pfam02867). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine).
Probab=20.20 E-value=49 Score=13.47 Aligned_cols=36 Identities=28% Similarity=0.370 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCC-----CCCCHHHCCCCCH
Q ss_conf 64879999999999864311123-----4772001023202
Q gi|254781170|r 252 GVLSPRQCWNRLKEEFVDLLIKP-----KSGAFSWLNELIW 287 (483)
Q Consensus 252 G~IS~R~v~~~~~~~~~~~~~~~-----~~~~~~fl~eL~W 287 (483)
|.-|.|+|++++......-..+. .++++.|.+||.|
T Consensus 41 ~E~S~rqv~~Rva~t~t~wG~k~GYF~se~da~~F~dEL~~ 81 (86)
T pfam08471 41 GETSLRQVFDRLVGTWTYWGWKGGYFATEEDAEAFYDELVY 81 (86)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 85739999999999999999878985999999999999999
Done!