Query 011172
Match_columns 492
No_of_seqs 177 out of 350
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:55:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011172hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1038 Mitochondrial/chloropl 100.0 1.5E-76 3.2E-81 636.8 34.8 469 1-492 89-595 (1088)
2 PF14700 RPOL_N: DNA-directed 100.0 2E-57 4.3E-62 463.4 20.6 302 143-466 1-318 (318)
3 PHA00452 T3/T7-like RNA polyme 100.0 7E-54 1.5E-58 477.9 32.7 306 139-491 3-318 (807)
4 COG5108 RPO41 Mitochondrial DN 100.0 7.2E-51 1.6E-55 427.9 22.7 323 143-492 251-593 (1117)
5 PF08849 DUF1819: Putative inn 41.8 51 0.0011 31.3 5.3 53 321-400 132-184 (189)
6 KOG3518 Putative guanine nucle 41.2 6.7 0.00014 40.7 -0.9 49 423-473 250-303 (521)
7 PF07739 TipAS: TipAS antibiot 34.7 40 0.00087 28.8 3.1 56 136-191 13-71 (118)
8 PF06152 Phage_min_cap2: Phage 20.8 2E+02 0.0044 30.3 5.9 51 141-196 310-360 (361)
9 PF11848 DUF3368: Domain of un 20.3 1.1E+02 0.0023 22.5 2.7 32 451-482 15-46 (48)
10 COG4989 Predicted oxidoreducta 19.4 44 0.00095 33.8 0.5 61 363-428 138-218 (298)
No 1
>KOG1038 consensus Mitochondrial/chloroplast DNA-directed RNA polymerase RPO41, provides primers for DNA replication-initiation [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=1.5e-76 Score=636.82 Aligned_cols=469 Identities=41% Similarity=0.665 Sum_probs=381.6
Q ss_pred Chhhhhhhh------hcccccc-CCC--------CCCccchhhhh---hcc-cccccccCCCCCCccccccccccccccc
Q 011172 1 MWRNLARQS------STRNFKF-SPS--------KVSQTTNFLKK---ITS-LETQTLLDSSCPLLGFRRTSFLSSQKSN 61 (492)
Q Consensus 1 ~~~~~~~~~------~~~~~~~-~~~--------~~~~~~~~~~~---~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (492)
||+|+..++ ..+.... +.+ .++--.++|+- ... |.... ..++++..|+++..+++-.|
T Consensus 89 ~~~~~l~~s~~~~t~~~~~~~~l~~~s~t~~l~~~~~~i~~~~S~~~~~lt~~~~~~-~~~p~~~~~~~~~~~l~~~n-- 165 (1088)
T KOG1038|consen 89 MWRNLLLKSFQNETMALRRHAALNPSSTTLGLLDPVEAISGIFSSLAKVLTTLRHKL-LVSPEHVRGIRQLLGLNNIN-- 165 (1088)
T ss_pred HhhhhHHHHhhhhhHHHHhhccCCchhhcccccchhhcchhhhhhhhhhhHHHhccc-ccCchhhhhhHHhhccchhh--
Confidence 799999998 5554443 222 11222344442 222 22222 35677788888888887666
Q ss_pred cCCCCCccCCCCccccccccccchhhhhhc---ccccCchHHHHHHHHHHHhhcccc-----cccccccccccccccCCC
Q 011172 62 LGQSNFTQSIYPFGVLTSRSYASAAEAIAS---ESELSGSEEVQELIDQFNEKGVSI-----LDSSSMLDKQPKKKGTGM 133 (492)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~ 133 (492)
+|.+...+.+| ..+||+-+++..-+ +.+++..+++.+++++|.++.... .......+...+....++
T Consensus 166 ----sF~~~~~~l~G-~~~g~s~a~e~~~~~~~~~~s~~~~~~~~~~~~m~ke~~~~~~~~~~~~~~~~~~~lk~v~k~~ 240 (1088)
T KOG1038|consen 166 ----SFPHSSEVLSG-LIKGSSLAGESENPTDQEGDSSNKQEINELVTKMEKEGNSLNQISSKFLEESRDLPLKAVRKGF 240 (1088)
T ss_pred ----cccchhhhhhc-ccccchHHHHHhCcccccccccchhhHHHHHhHhhhhhhhhhHHHHHHHHHHhcccHHHHHHhc
Confidence 45566666666 67888444555444 333445779999999999987431 111222223335666677
Q ss_pred ChH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHcccCCCchh-HHHHHHHHHHHHHHHHHHHHHHHhhc--cCcc
Q 011172 134 GTA-KYYMLKRRQIKIETEAWEQAAKEYQ-DLLADMCEQKLAPNLPY-VKSLFLGWFEPLRDAIAKDQATAQDK--WKHM 208 (492)
Q Consensus 134 ~~~-~~~~l~~rQl~LE~ea~e~A~er~r-~~~e~~~~~g~a~~l~~-~k~Ll~~W~~~L~~aI~~e~~~~~~~--~~r~ 208 (492)
+.. +|..+.+||..+|+++|+.|+++|+ +...+||+..+++++|+ +++|+++||++|+++|++|++.++.. +.|.
T Consensus 241 ~~~~d~~~l~~Rq~~~e~~~~e~a~e~~k~el~~~~c~~~l~~~lp~~lk~lf~~W~~~l~~ai~ee~n~~r~~~~~~r~ 320 (1088)
T KOG1038|consen 241 GDFKDFFNLDRRQVKLETEAWERAAEEWKIELESDMCEGSLAPNLPYNLKSLFLGWFKPLRDAIKEEINLLRALVRKGRL 320 (1088)
T ss_pred cchHhHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 766 8999999999999999999999999 78889999999999999 99999999999999999999999886 7899
Q ss_pred ccccccccCChhHHHHHHHHHHHHHhccCC--CCccHHHHHHHHHHHHHHHHHHHHhhhhhhccccccCCCCCCCCCCCC
Q 011172 209 TYAPYFNNLPADMMAVITMHKLVGLLMTNA--GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTN 286 (492)
Q Consensus 209 ~y~pyL~~L~~d~LA~Iti~~~l~~l~~~~--~~~~v~~la~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~ 286 (492)
.|+|||++||++++|+|||+++|+++++|+ +|+++++++..||++||+|+++..+.++..+.+..+
T Consensus 321 ~Y~p~L~lL~a~k~aviti~el~~ll~tg~~~~~~~v~~aa~~~G~aveqe~ri~~~lq~~~k~~~~~------------ 388 (1088)
T KOG1038|consen 321 NYAPFLKLLDADKMAVITIHELMGLLMTGGETGGVRVVQAAKSLGRAVEQEFRIEQFLQRKTKNKAGD------------ 388 (1088)
T ss_pred ccchHHHhcChhhHHHHHHHHHHhhhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccch------------
Confidence 999999999999999999999999999987 899999999999999999999999987754322211
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCc
Q 011172 287 DPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPA 366 (492)
Q Consensus 287 d~~~~~~~~~~lrk~~~~l~k~~k~~~~~~~~~~~~~~~~W~~~~~~kVGs~Li~lLietakI~v~~~~~~~~~~~~~PA 366 (492)
.....++....++.+..++++.++.+.......++...+||..++++||++||++||++++|+++++++.++.++.+||
T Consensus 389 -~~~~~ke~~~~~~~v~~l~~~~k~~~~~~~~~~~~~~~pWp~~v~~kvGs~L~~lL~~~aki~~~~~~~~~~~~~~~pa 467 (1088)
T KOG1038|consen 389 -SYCELKELGKSRKEVRQLVQNLKLSQRLSGPESHLSEKPWPSAVQAKVGSRLIELLMQVAKIQVPADQPDTKLPDERPA 467 (1088)
T ss_pred -HHHHHHHhhcccHHHHHHHHHHHHHHHhcccccccccCCccHHHHHHHHHHHHHHHHHHhcCCCcccCcCcCccccchh
Confidence 1122345556677788777777777766666666778999999999999999999999999999999999999999999
Q ss_pred eEEEEeeccccccCCeEEEEEEeCHHHHHHHHhhcccccCCCCceeeCCCCCCCCCCccccccccchhcccCcHHHHHHH
Q 011172 367 FVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETI 446 (492)
Q Consensus 367 F~H~~~~~~~~~~~gkk~GvI~~hp~l~~~l~~~~~~~~~p~LPMLvPPkPWts~~~GGYL~~~s~lmR~~g~~~Q~~~l 446 (492)
|+|+|++ ++.++.|++||+|+|||.+.+.|++.+.|+..+++||||||+||++|++||||++|++||||||+++|+.|+
T Consensus 468 f~h~f~~-~n~~~~~~~~g~ie~~pll~r~leks~~~~~~~~vPMLvpPkpWt~~~~Ggyl~~~s~lmRt~g~~~Q~~~l 546 (1088)
T KOG1038|consen 468 FVHTFQV-TNGQKGGRKYGVIECHPLLSRGLEKSALHFVPPLVPMLVPPKPWTGYDSGGYLFLPSYLMRTHGAKEQVDYL 546 (1088)
T ss_pred hhhheee-ecccccceeeeeeecCHHHHHHhhhhhccccccccccccCCCCCCCCCCCceEecchhhhhcCCcHHHHHHH
Confidence 9999995 455556889999999999999999999899989999999999999999999999999999999999999977
Q ss_pred HcC-CCCCchhHHHHHHHhcCCCceecHHHHHHHHHHHh---ccCCCCCC
Q 011172 447 KMT-PRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLM---CSFCGISS 492 (492)
Q Consensus 447 ~~a-~~~qL~~Vf~aLN~LGstpWrIN~~VLdvI~~~~~---~~~l~IP~ 492 (492)
..+ +.++|++||||||+||+|+||||.+|||+|+.+ | +++++||+
T Consensus 547 lkas~~~~l~~v~daL~~LG~t~WrVN~rvldvV~ri-w~~Gg~~~~~v~ 595 (1088)
T KOG1038|consen 547 LKASPPGQLDPVFDALDTLGNTKWRVNRRVLDVVIRI-WQNGGCFLLIVP 595 (1088)
T ss_pred HhcCChhhhHHHHHHHHHhcCCCeeecchHHHHHHHH-HhcCCCccCCCC
Confidence 555 789999999999999999999999999999776 6 88998885
No 2
>PF14700 RPOL_N: DNA-directed RNA polymerase N-terminal; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D ....
Probab=100.00 E-value=2e-57 Score=463.44 Aligned_cols=302 Identities=31% Similarity=0.534 Sum_probs=223.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCchhHHHHHHHHHHHHHHHHHHHHHHHh----hccCccccccccccCC
Q 011172 143 RRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQ----DKWKHMTYAPYFNNLP 218 (492)
Q Consensus 143 ~rQl~LE~ea~e~A~er~r~~~e~~~~~g~a~~l~~~k~Ll~~W~~~L~~aI~~e~~~~~----~~~~r~~y~pyL~~L~ 218 (492)
+||++||.++++.|++||++..+++.++|.+++++++++++++|+++|+++|+++++.+. ..+.++.|+|||+.||
T Consensus 1 ~rQ~~lE~~~~~~a~~r~~~~~~~~~~~g~~~~~~~~~~l~~~w~~~L~~~i~~~~~~~~~~~~~~~~~~~~~p~L~~l~ 80 (318)
T PF14700_consen 1 ERQLELEEESYEAARERWREEFEKAQKRGRASSLPYLQALMWQWYEPLAEAIQEEQEKLKASSKKRGRRAAYGPFLKLLP 80 (318)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGCCCCCHHHHHHHHHHHHHHHHHHHHHHH--HCCCTT--HCCHHCCTS-
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcchHHHHHHcCC
Confidence 589999999999999999999999999999999999999999999999999999999875 3456899999999999
Q ss_pred hhHHHHHHHHHHHHHhccCC---CCccHHHHHHHHHHHHHHHHHHHHhhhhhhccccccCCCCCCCCCCCCChHHHHHHH
Q 011172 219 ADMMAVITMHKLVGLLMTNA---GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQ 295 (492)
Q Consensus 219 ~d~LA~Iti~~~l~~l~~~~---~~~~v~~la~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~d~~~~~~~~ 295 (492)
+|++|+|||+++|+++++++ +|+++++++.+||++||+|++++++.+..++.+....+.... ......
T Consensus 81 ~e~lA~Iti~~~l~~~~~~~~~~~g~~~~~~~~~IG~aVe~E~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~------- 151 (318)
T PF14700_consen 81 PEKLAVITIREVLNLLSSSEGYSKGMKLTRLAIAIGRAVEQEYRFQQLEKAEPKYYKKLKKNFKK--KRSKSQ------- 151 (318)
T ss_dssp HHHHHHHHHHHHHHHHTTSSSE----EHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCHHHHCHC--CSTSCH-------
T ss_pred HHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh--cccchh-------
Confidence 99999999999999998543 567999999999999999999999988766544321110000 000000
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhCCCCCC--CCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceEEEEee
Q 011172 296 EKLKKRVTSLIKKQKLQQVRGIVKGHVDSK--PWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKS 373 (492)
Q Consensus 296 ~~lrk~~~~l~k~~k~~~~~~~~~~~~~~~--~W~~~~~~kVGs~Li~lLietakI~v~~~~~~~~~~~~~PAF~H~~~~ 373 (492)
.++.+...++..+........ ..++. +|+..++++||++|+++|+++|+|+++..++.+ ...+|||+|+|++
T Consensus 152 --~~r~~~~~~~~~~~~~~~~~~--~~~~~~~~W~~~~~~~vG~~Ll~~l~~~~~i~~~~~~~~~--~~~~paf~~~~~~ 225 (318)
T PF14700_consen 152 --QKRHVWQLLKNRKDSSGKPSL--EEEWSDSPWPSDIRAKVGSFLLELLMETAKIPVERKDPET--SEEQPAFYHSYRY 225 (318)
T ss_dssp --HCHHHHHHHHHHHSHSS-STT--T-TCCC--SCHHHHHHHHHHHHHHHHHCTCEEEEEESTT-------BSEEEEE--
T ss_pred --hHHHHHHHHHHHHHhcccccc--ccccccCCCCHHHHHHHHHHHHHHHHhheeeccccCCccc--cccccchhhhhcc
Confidence 001111111111100000011 12343 499999999999999999999999998755433 6899999999998
Q ss_pred ccccccCCeEEEEEEeCHHHHHHHHhhccc-----ccCC-CCceeeCCCCCCCCCCccccccccchhcccCcHHHHHHHH
Q 011172 374 FTKEALKGRRYGVIECDPLVRKGLEKTGRH-----MIIP-YMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIK 447 (492)
Q Consensus 374 ~~~~~~~gkk~GvI~~hp~l~~~l~~~~~~-----~~~p-~LPMLvPPkPWts~~~GGYL~~~s~lmR~~g~~~Q~~~l~ 447 (492)
. +|+++|+|+|||.+.+++++.... ++ | +|||||||+||+++++||||+.++++||+++. .|..|++
T Consensus 226 ~-----~~~~~g~i~~~~~~~~~l~~~~~~~~~~~~~-~~~lPMlvpP~PW~~~~~GGYl~~~~~l~R~~~~-~~~~~~~ 298 (318)
T PF14700_consen 226 R-----KGKKVGVIKPHPELVKLLSDEPEKSLLQATF-PRYLPMLVPPKPWTSPNDGGYLLSPTPLMRTKDS-EQQQYLK 298 (318)
T ss_dssp ------TTT-EEEEEE-HHHHHHHHHHCH---CCCCC-CCCS-BSS--EEECCTCCEESSSSSEBSEE-STT-HHCHHHH
T ss_pred c-----cCceEEEEeeCHHHHHHHHhhhhhhhhhhcc-cccCcCCCCCCCCcCCCcceeeeeCchhhcccch-hhHHHHH
Confidence 4 699999999999999999997652 13 6 99999999999999999999999999999877 6666665
Q ss_pred cC-CCCCchhHHHHHHHhcC
Q 011172 448 MT-PRSQLEPVFQVSRVLYS 466 (492)
Q Consensus 448 ~a-~~~qL~~Vf~aLN~LGs 466 (492)
++ .+++|++||+|||+||+
T Consensus 299 ~~~~~~~l~~v~~~Ln~Lg~ 318 (318)
T PF14700_consen 299 KALRRGDLDPVFDALNALGS 318 (318)
T ss_dssp HTTTCCGGHHHHHHHHHHHT
T ss_pred HHccccchHHHHHHHHHhcC
Confidence 54 68999999999999996
No 3
>PHA00452 T3/T7-like RNA polymerase
Probab=100.00 E-value=7e-54 Score=477.87 Aligned_cols=306 Identities=18% Similarity=0.242 Sum_probs=249.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhccCccccccccccCC
Q 011172 139 YMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLP 218 (492)
Q Consensus 139 ~~l~~rQl~LE~ea~e~A~er~r~~~e~~~~~g~a~~l~~~k~Ll~~W~~~L~~aI~~e~~~~~~~~~r~~y~pyL~~L~ 218 (492)
.+|.+||++||.+++++|++||++++++++++|.++++|++++++.+|+++|+++|+++++.++..+.++.|+|||+++|
T Consensus 3 ~~l~~rQ~~lE~~~~~~a~~r~~~~~~~~~~~g~~~~~~~~~~l~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~L~~~~ 82 (807)
T PHA00452 3 EDLAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRAAKARGLLRLVD 82 (807)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhHHHHHcCC
Confidence 46889999999999999999999999999999999999999999999999999999999999877778899999999999
Q ss_pred hhHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHHHHHHhhhhhhccccccCCCCCCCCCCCCChHHHHHHHHHH
Q 011172 219 ADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKL 298 (492)
Q Consensus 219 ~d~LA~Iti~~~l~~l~~~~~~~~v~~la~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~d~~~~~~~~~~l 298 (492)
||++|+|||+++|++++++ ++.++++++++||++||+|++++++++++++.+.+..+ ...
T Consensus 83 ~d~lA~Iti~~~l~~l~~~-~~~~~~~~~~~iG~aie~E~r~~~~~~~~~~~~~~~~~-------------------~~~ 142 (807)
T PHA00452 83 PEVLAVITLKVTLDMLLSK-ETPTAQAVATAIGRAIEDEIRFGRIEDLNPKYFKKVVE-------------------YLK 142 (807)
T ss_pred HHHHHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHHHH-------------------HHH
Confidence 9999999999999999884 46799999999999999999999998877654332110 112
Q ss_pred HHHHHHHHHHHH-HHHHHHhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHc-cccCCCCCCCCCCCCccCceEEEEeeccc
Q 011172 299 KKRVTSLIKKQK-LQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETA-YIQPPVDQLGDSPPDIRPAFVHTLKSFTK 376 (492)
Q Consensus 299 rk~~~~l~k~~k-~~~~~~~~~~~~~~~~W~~~~~~kVGs~Li~lLieta-kI~v~~~~~~~~~~~~~PAF~H~~~~~~~ 376 (492)
+++.+...++.+ ...+...+... ++.+|+.+++++||++|+++|++++ .+++.. + ..
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~W~~~~~~kvG~~Ll~~l~~~a~~~~~~~-~---------------~~---- 201 (807)
T PHA00452 143 RSRTGSVYHIAFMMVVEADMVLLG-EWDPWPKEDYIHVGKWLLEALIESTGLVELVR-H---------------TG---- 201 (807)
T ss_pred hcccchHHHHHHHHHHHHHhhhcc-CCCCCCHHHHHHHHHHHHHHHHHhhCceeeee-c---------------cc----
Confidence 222232211111 12223333322 4889999999999999999999997 443321 1 01
Q ss_pred cccCCeEEEEEEeCHHHHHHHHhhccc--ccCC-CCceeeCCCCCCCCCCccccccc---cchhcccCcHHHHHHHHcCC
Q 011172 377 EALKGRRYGVIECDPLVRKGLEKTGRH--MIIP-YMPMLVPPLNWRGYNRGGHFFLP---SYVMRTHGARQQRETIKMTP 450 (492)
Q Consensus 377 ~~~~gkk~GvI~~hp~l~~~l~~~~~~--~~~p-~LPMLvPPkPWts~~~GGYL~~~---s~lmR~~g~~~Q~~~l~~a~ 450 (492)
.++|+++|+|+|||.+.+++++...+ .+.| +|||||||+||+++++||||+.+ +.+||+++...+..+.+
T Consensus 202 -~~~~~~~g~i~~~~~~~~~l~~~~~~~~~~~p~~lPMlvpP~pW~~~~~GGyl~~~~~~~~~~~~~~~~~~~~~~~--- 277 (807)
T PHA00452 202 -GNGGKDHEYLELSEEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHTEGRRPLAPLVRKTKKALRRYRQ--- 277 (807)
T ss_pred -CCCCceeeEEEeCHHHHHHHHhhhhhhhhcCcccCceeccCcccCCCCCCCceeccccccceeEecCHHHHHHHHh---
Confidence 13578899999999999999997655 3567 99999999999999999999864 67788888777766654
Q ss_pred CCCchhHHHHHHHhcCCCceecHHHHHHHHHHHh--ccCCCCC
Q 011172 451 RSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLM--CSFCGIS 491 (492)
Q Consensus 451 ~~qL~~Vf~aLN~LGstpWrIN~~VLdvI~~~~~--~~~l~IP 491 (492)
++|+.||+|||+||+|||+||.+|||+|.++ | ++++|+|
T Consensus 278 -~~l~~v~~aLN~Lg~t~w~IN~~vl~v~~~~-~~~~~~~~~~ 318 (807)
T PHA00452 278 -KQMPEVYKAVNALQNTAWRINKDVLAVVNEV-VNWGPVGDVL 318 (807)
T ss_pred -hhhHHHHHHHHHHhcCCceecHHHHHHHHHH-HhcCCcccCC
Confidence 7999999999999999999999999988665 7 5455655
No 4
>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]
Probab=100.00 E-value=7.2e-51 Score=427.88 Aligned_cols=323 Identities=20% Similarity=0.314 Sum_probs=272.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCchhHHHHHHHHHHHHHHHHHHHHHH-Hhh---------ccCcccccc
Q 011172 143 RRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQAT-AQD---------KWKHMTYAP 212 (492)
Q Consensus 143 ~rQl~LE~ea~e~A~er~r~~~e~~~~~g~a~~l~~~k~Ll~~W~~~L~~aI~~e~~~-~~~---------~~~r~~y~p 212 (492)
+||..||..++..|.|+|+..+++..++|...--+-+.+.++.||..+..+.++|+.. ..+ .+.|..|+|
T Consensus 251 ~rqk~le~~ai~~a~E~wk~~~e~~~~rg~~~~eKN~~~~~~swy~~i~~l~keeI~~l~e~l~~~~sl~K~~~rl~ygp 330 (1117)
T COG5108 251 ERQKWLEKSAIALAEEMWKAGIERFEKRGEKNREKNAEASNLSWYRMIIHLHKEEIAGLLEALLAEASLGKAGKRLTYGP 330 (1117)
T ss_pred HHHHHHHHhHHHHHHHHHHhhHHHHHhccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccCeecccc
Confidence 5899999999999999999999999998876555678999999999999999999874 221 346899999
Q ss_pred ccccCChhHHHHHHHHHHHHHhccCC--CCccHHHHHHHHHHHHHHHHHHHHhhhhhhccccccCCCCCCCCCCCCChHH
Q 011172 213 YFNNLPADMMAVITMHKLVGLLMTNA--GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEK 290 (492)
Q Consensus 213 yL~~L~~d~LA~Iti~~~l~~l~~~~--~~~~v~~la~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~d~~~ 290 (492)
||++++++++|+|||.+++++..+++ .|++++.+...+|++||.|+..++++..+++.|....++ ++
T Consensus 331 yLkl~d~~k~a~lTi~el~~l~s~~~~~~gmr~t~l~i~lg~~vE~Ef~seq~~~~e~~ay~d~~kk---------~p-- 399 (1117)
T COG5108 331 YLKLADLDKVAHLTIRELFDLVSMRRYDRGMRLTPLSIRLGAMVEDEFFSEQFKGHEKDAYEDARKK---------IP-- 399 (1117)
T ss_pred ceeccCcccchhhhHHHHHHhhccccccccceeehhHHHHHHHHHHHHHHHHHhhhhhHHHHHHhhc---------Ch--
Confidence 99999999999999999999988766 789999999999999999999999988776655432221 11
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCC--CCCccCceE
Q 011172 291 LIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDS--PPDIRPAFV 368 (492)
Q Consensus 291 ~~~~~~~lrk~~~~l~k~~k~~~~~~~~~~~~~~~~W~~~~~~kVGs~Li~lLietakI~v~~~~~~~~--~~~~~PAF~ 368 (492)
+..++.+++ ++...+.......+|.+||+++++|||++++.+|+.+|+|.+...++.++ .....|||.
T Consensus 400 -----~~f~~aV~n-----~rs~tr~~~~~~~~~~~Wpq~i~akvGsv~l~lll~vaki~v~~id~~t~~~l~ge~~af~ 469 (1117)
T COG5108 400 -----EQFHNAVHN-----KRSMTRHAKHKGAEWQDWPQDIKAKVGSVALCLLLSVAKIEVKLIDIATEQTLKGEFEAFR 469 (1117)
T ss_pred -----HHHHHHHHH-----HHhhhhhhhhcCcchhcChHHHHHHhhHHHHHHHHHhhhheeEeeechhhchhhhhHHHHH
Confidence 123333333 11111222222467889999999999999999999999999988775544 347899999
Q ss_pred EEEeeccccccCCeEEEEEEeCHHHHHHHHhhccc-ccCC-CCceeeCCCCCCCCCCccccccccchhcccCcHHHHHHH
Q 011172 369 HTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRH-MIIP-YMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETI 446 (492)
Q Consensus 369 H~~~~~~~~~~~gkk~GvI~~hp~l~~~l~~~~~~-~~~p-~LPMLvPPkPWts~~~GGYL~~~s~lmR~~g~~~Q~~~l 446 (492)
|+|+|. +|+++|||.+|..+..++.+..+- -+.| +|||||||+|||++..|||++.+++++|++++.+|-.|+
T Consensus 470 h~yqyh-----Ng~kigvv~~h~tl~~ll~~~~~~a~l~PqlLPmLV~PkPWtsw~~GGY~y~r~~llRlk~t~eqv~yl 544 (1117)
T COG5108 470 HSYQYH-----NGTKIGVVATHETLDWLLTENSRLAPLSPQLLPMLVPPKPWTSWFRGGYWYGRVRLLRLKKTGEQVRYL 544 (1117)
T ss_pred Hhhhhc-----CCceeEEEeeHHHHHHHhhcccccCCCChhhhccccCCCCCcCcccCceeeccceeeeecCcHHHHHHH
Confidence 999984 899999999999999999876543 4778 999999999999999999999999999999999999999
Q ss_pred HcCC-CCCchhHHHHHHHhcCCCceecHHHHHHHHHHHh---ccCCCCCC
Q 011172 447 KMTP-RSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLM---CSFCGISS 492 (492)
Q Consensus 447 ~~a~-~~qL~~Vf~aLN~LGstpWrIN~~VLdvI~~~~~---~~~l~IP~ 492 (492)
..++ .+||+.||+++|+||+|||+||.+|++++.. +| .+||+||+
T Consensus 545 ~~asengd~d~vy~~in~lg~t~W~iN~rvf~V~~~-~Wn~ge~fl~IP~ 593 (1117)
T COG5108 545 LMASENGDMDKVYHSINALGNTAWSINHRVFEVMAS-LWNNGETFLCIPQ 593 (1117)
T ss_pred HHhhhcCChHHHHHHHHHhccCchhhhHHHHHHHHH-HHhCCCceeccCc
Confidence 8874 7999999999999999999999999998865 48 89999995
No 5
>PF08849 DUF1819: Putative inner membrane protein (DUF1819); InterPro: IPR014948 These proteins are functionally uncharacterised. Several are annotated as putative inner membrane proteins. ; PDB: 3BHW_A.
Probab=41.84 E-value=51 Score=31.32 Aligned_cols=53 Identities=17% Similarity=0.338 Sum_probs=32.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceEEEEeeccccccCCeEEEEEEeCHHHHHHHHhh
Q 011172 321 HVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKT 400 (492)
Q Consensus 321 ~~~~~~W~~~~~~kVGs~Li~lLietakI~v~~~~~~~~~~~~~PAF~H~~~~~~~~~~~gkk~GvI~~hp~l~~~l~~~ 400 (492)
+.....|+..++-||++.+..+|.+.+.++-. +.+++--+.++|.+...+...
T Consensus 132 ~~~i~~WSdsT~~Kl~~~~~~~L~eaGlL~~~---------------------------~~~~i~~~~l~~~~~~~l~~~ 184 (189)
T PF08849_consen 132 DPEIASWSDSTIKKLRQVLFRILREAGLLEGS---------------------------RSKKIQPPLLSPEVREYLKRN 184 (189)
T ss_dssp -TTS----HHHHHHHHHHHHHHHHHTTSBS-T---------------------------TT-BB------HHHHHHHHHT
T ss_pred CCcccccCHHHHHHHHHHHHHHHHHcCCccCC---------------------------CCCeeecCcCCHHHHHHHHHh
Confidence 35567899999999999999999999998431 234454567888888888764
No 6
>KOG3518 consensus Putative guanine nucleotide exchange factor [General function prediction only]
Probab=41.17 E-value=6.7 Score=40.68 Aligned_cols=49 Identities=14% Similarity=0.048 Sum_probs=31.9
Q ss_pred Cccccccccc-hhcccCcHHHHHHHHcC----CCCCchhHHHHHHHhcCCCceecH
Q 011172 423 RGGHFFLPSY-VMRTHGARQQRETIKMT----PRSQLEPVFQVSRVLYSSIFYDLF 473 (492)
Q Consensus 423 ~GGYL~~~s~-lmR~~g~~~Q~~~l~~a----~~~qL~~Vf~aLN~LGstpWrIN~ 473 (492)
-|+||+.|.. +++.|=- ..+..+.. .+..++.|.+|.++++++||+||-
T Consensus 250 l~ayllkpvqrilkyhlf--le~i~k~l~~~thpeel~qvk~ahd~m~~qa~~ind 303 (521)
T KOG3518|consen 250 LGAYLLKPVQRILKYHLF--LEEIEKHLDKDTHPEELDQVKDAHDTMQRQAAHIND 303 (521)
T ss_pred hhHHHHHHHHHHHHHHHH--HHHHHhcCCCCCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 4899998632 3332211 11222222 245789999999999999999984
No 7
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=34.70 E-value=40 Score=28.77 Aligned_cols=56 Identities=27% Similarity=0.586 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HcccCCCchhHHHHHHHHHHHHH
Q 011172 136 AKYYMLKRRQIKIETEAWEQAAKEYQDLLADMC---EQKLAPNLPYVKSLFLGWFEPLR 191 (492)
Q Consensus 136 ~~~~~l~~rQl~LE~ea~e~A~er~r~~~e~~~---~~g~a~~l~~~k~Ll~~W~~~L~ 191 (492)
..|.+..++...|-.+-++....+|.++..++. +.|..++.+-++.++.+|+.-+.
T Consensus 13 ~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~l~~~~~~g~~p~s~evq~l~~~~~~~~~ 71 (118)
T PF07739_consen 13 EAYAESEERLASLSKEEWQELQKEWDELFAELAALMEEGVDPDSPEVQELAERWMELIN 71 (118)
T ss_dssp --------------------TTHHHHHHHHHHHHHHHHT--TT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHH
Confidence 445555445555666666666666776655554 56888999999999999999887
No 8
>PF06152 Phage_min_cap2: Phage minor capsid protein 2; InterPro: IPR009319 This entry is represented by Bacteriophage A118, Gp4, the minor capsid protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=20.80 E-value=2e+02 Score=30.35 Aligned_cols=51 Identities=18% Similarity=0.130 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCchhHHHHHHHHHHHHHHHHHH
Q 011172 141 LKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAK 196 (492)
Q Consensus 141 l~~rQl~LE~ea~e~A~er~r~~~e~~~~~g~a~~l~~~k~Ll~~W~~~L~~aI~~ 196 (492)
..++|..+| .++.+|++.+.-+...|...+....+..+..|...+++.|++
T Consensus 310 ~~Q~QR~~E-----R~IR~~Kr~~~~~~~~~d~~~~~~~~~~~r~~q~~~r~~~~~ 360 (361)
T PF06152_consen 310 ATQKQRYLE-----RQIRKWKRRLAAAEALGDDENIQKAKAKVRQQQAKYRDFIKE 360 (361)
T ss_pred hhHHHHHHH-----HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 446777666 567777777666666665445567888899999999988864
No 9
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=20.30 E-value=1.1e+02 Score=22.54 Aligned_cols=32 Identities=19% Similarity=0.039 Sum_probs=27.7
Q ss_pred CCCchhHHHHHHHhcCCCceecHHHHHHHHHH
Q 011172 451 RSQLEPVFQVSRVLYSSIFYDLFNLYRLIINF 482 (492)
Q Consensus 451 ~~qL~~Vf~aLN~LGstpWrIN~~VLdvI~~~ 482 (492)
++-++.+-.+|+.|....++|+.++++.+++.
T Consensus 15 ~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~ 46 (48)
T PF11848_consen 15 RGLISEVKPLLDRLQQAGFRISPKLIEEILRR 46 (48)
T ss_pred cCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence 36677888899999999999999999988764
No 10
>COG4989 Predicted oxidoreductase [General function prediction only]
Probab=19.42 E-value=44 Score=33.84 Aligned_cols=61 Identities=33% Similarity=0.562 Sum_probs=46.0
Q ss_pred ccCceEEEEeeccccccCCeEEEEEEeCHHHHHHHHhhccc------c-cCC-CCcee------------eCCCCCCCCC
Q 011172 363 IRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRH------M-IIP-YMPML------------VPPLNWRGYN 422 (492)
Q Consensus 363 ~~PAF~H~~~~~~~~~~~gkk~GvI~~hp~l~~~l~~~~~~------~-~~p-~LPML------------vPPkPWts~~ 422 (492)
.--||.|.++ +|+.|.+||=..+|.-.++|+..... + ++| +.||+ |+|.+|+-..
T Consensus 138 VAeAf~~L~~-----sGKVr~fGVSNf~p~Q~~LL~s~l~~~LvtNQlelS~~~~~~~~DGtLd~~q~~~v~pmaWSpl~ 212 (298)
T COG4989 138 VAEAFTHLHK-----SGKVRHFGVSNFNPAQFELLQSRLPFTLVTNQLELSPLHTPMLLDGTLDYCQQLRVRPMAWSPLG 212 (298)
T ss_pred HHHHHHHHHh-----cCCeeeeecCCCCHHHHHHHHHhccchhhhcceeeccccccccccchHHHHHHcCCCcccccccC
Confidence 3457777666 36789999999999999999886321 1 456 78887 7999998877
Q ss_pred Cccccc
Q 011172 423 RGGHFF 428 (492)
Q Consensus 423 ~GGYL~ 428 (492)
.||-..
T Consensus 213 gG~~F~ 218 (298)
T COG4989 213 GGGLFL 218 (298)
T ss_pred CCcccc
Confidence 776554
Done!