Query 043303
Match_columns 1639
No_of_seqs 32 out of 34
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 03:38:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043303.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043303hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13766 Hef nuclease; Provisi 98.6 7.1E-05 1.5E-09 91.9 31.9 512 616-1182 207-765 (773)
2 TIGR00596 rad1 DNA repair prot 98.2 0.00019 4.2E-09 90.2 24.8 164 984-1167 603-794 (814)
3 COG1948 MUS81 ERCC4-type nucle 93.8 1.1 2.4E-05 51.1 13.9 182 958-1169 28-221 (254)
4 COG1111 MPH1 ERCC4-like helica 93.5 0.51 1.1E-05 57.9 11.4 176 614-802 205-399 (542)
5 PF02732 ERCC4: ERCC4 domain; 86.2 2.5 5.3E-05 41.5 7.1 116 979-1103 11-141 (143)
6 KOG2841 Structure-specific end 71.9 1.1E+02 0.0025 35.6 14.9 193 953-1183 51-247 (254)
7 PRK02842 light-independent pro 64.3 5.5 0.00012 47.5 3.2 82 706-803 239-323 (427)
8 KOG0442 Structure-specific end 57.5 1.4E+02 0.003 39.8 13.6 164 984-1169 669-860 (892)
9 TIGR01279 DPOR_bchN light-inde 51.4 9.8 0.00021 45.3 2.4 76 709-803 231-306 (407)
10 cd01979 Pchlide_reductase_N Pc 50.3 12 0.00027 44.1 3.0 75 709-803 233-308 (396)
11 COG2710 NifD Nitrogenase molyb 34.9 35 0.00076 41.7 3.6 89 694-798 237-340 (456)
12 PF10087 DUF2325: Uncharacteri 30.3 70 0.0015 31.1 4.1 59 773-840 1-60 (97)
13 PRK14478 nitrogenase molybdenu 26.3 42 0.0009 41.1 2.3 85 706-802 268-355 (475)
14 cd03466 Nitrogenase_NifN_2 Nit 25.4 1.1E+02 0.0024 37.0 5.5 72 709-798 256-327 (429)
15 cd01974 Nitrogenase_MoFe_beta 25.0 41 0.0009 40.4 1.9 78 707-802 257-334 (435)
16 PRK02910 light-independent pro 24.1 1.3E+02 0.0027 37.6 5.7 85 707-802 240-325 (519)
17 TIGR01282 nifD nitrogenase mol 23.3 51 0.0011 40.4 2.2 79 707-801 285-365 (466)
18 TIGR01278 DPOR_BchB light-inde 22.8 1.2E+02 0.0026 37.6 5.2 87 707-802 240-327 (511)
19 CHL00073 chlN photochlorophyll 22.2 45 0.00098 41.2 1.5 78 708-804 270-347 (457)
20 cd01973 Nitrogenase_VFe_beta_l 21.7 75 0.0016 38.9 3.2 75 707-799 258-333 (454)
21 TIGR01286 nifK nitrogenase mol 21.6 49 0.0011 41.3 1.6 76 707-801 317-393 (515)
No 1
>PRK13766 Hef nuclease; Provisional
Probab=98.55 E-value=7.1e-05 Score=91.88 Aligned_cols=512 Identities=13% Similarity=0.162 Sum_probs=260.1
Q ss_pred ceeEEEeecccchhHHHHHHHHHHHHhhhhccccccccccCcccccccCcchhhhhhhhhhccccccc---cC-CCCCch
Q 043303 616 QWDVTLYKVKLSDDILALIDIFKKSYLAIVHNETELSSFVTSDDFKLLSLPKQRLMDCINRKRFQKAN---SH-GDGNCM 691 (1639)
Q Consensus 616 ~~~i~lh~V~lSd~I~~Li~~~~ksYls~l~~~te~~h~~d~d~~kll~i~K~kL~d~I~~~~s~~~~---~~-~~~~~m 691 (1639)
...++...|.+++.+..+...+..-+..-+++-..+...... . ..+.+..|...-+. .+... .| .+..+.
T Consensus 207 ~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~~~~~~~~-~---~~~~~~~l~~~~~~--~~~~l~~~~~~~~~~~~ 280 (773)
T PRK13766 207 KVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELGVIVSI-S---PDVSKKELLGLQKK--LQQEIANDDSEGYEAIS 280 (773)
T ss_pred cceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHHCCCcccC-C---CCcCHHHHHHHHHH--HHHHhhcCchHHHHHHH
Confidence 345666678899998887776666555444432222211000 0 01223222222110 01110 01 111111
Q ss_pred hHHHHHHHHhhhhhheeeccchhhhHHhhhhhhccccccchhhhHHHHHhhcc-----ccccccCCCCchHHHHHHHhhc
Q 043303 692 ALITLCSIKLMAWYTCFYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADG-----KIDKETSSHPSLLVIQGILQSN 766 (1639)
Q Consensus 692 ~li~L~aiKQaA~ylcfyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~-----kve~~~~sHPsL~~Iq~iL~s~ 766 (1639)
-++-+.-+.++..++.-+|.-+..-|+..+.... ..++.....+.++.++.. ..+.-.+.|||+..+..+|+..
T Consensus 281 ~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~ 359 (773)
T PRK13766 281 ILAEAMKLRHAVELLETQGVEALRRYLERLREEA-RSSGGSKASKRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQ 359 (773)
T ss_pred HHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhc-cccCCcHHHHHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHH
Confidence 2223344567777888888877777776655322 222334444444443332 2222367899999999999887
Q ss_pred cc-cCCceEEEEe-chhHHHHHHHHHHhcCCccccccCccccc--------CCccccccccccccccccCCCcceeeecc
Q 043303 767 SS-QSNLKVLIVA-EQSFWWSLKCLVMSMGLSCSELQNFYTHV--------DQPDVTKVYGSASAKMTDLPISDCLMVSH 836 (1639)
Q Consensus 767 ~~-~~~~K~LIVa-d~~Fwlslk~~L~sMg~s~~el~~~~~s~--------~~~D~~e~~~f~~~~~~~L~~SDCLL~s~ 836 (1639)
.. .++.|+||.+ .+-.=--|.+.|..+|..+..+.+...+. .+....+. |.. ...++|+++.
T Consensus 360 ~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~--F~~------g~~~vLvaT~ 431 (773)
T PRK13766 360 LGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDK--FRA------GEFNVLVSTS 431 (773)
T ss_pred HhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHH--HHc------CCCCEEEECC
Confidence 64 3578888888 55555566788899999988777643211 11123332 332 2467777775
Q ss_pred cccccCCCcccceeEEEecCCCCCccccccCccccCCCc--ceEEEEEe--CchhhhHhhhcCCCCChhh--HHHhhcCC
Q 043303 837 ESVSASFPFKKFSLILEYGGSHGSSRISALSPKVAGLPH--LHFLKVEL--DDSSASRALCEGLDVPENM--EVELLDLL 910 (1639)
Q Consensus 837 ~hI~~sFPf~~F~iIveYggs~~ss~i~~ls~kLa~~p~--lHfL~Vel--D~~~a~~alceg~~~pq~~--le~~Ln~~ 910 (1639)
-+.++.=+..=..+|-|.++....++-.-.-|.+-... +++|..+= |......++-.--.+-..+ ....+. .
T Consensus 432 -~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~~~v~~l~~~~t~ee~~y~~~~~ke~~~~~~l~~~k~~l~-~ 509 (773)
T PRK13766 432 -VAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEEGRVVVLIAKGTRDEAYYWSSRRKEKKMKEELKNLKGILN-K 509 (773)
T ss_pred -hhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCCCEEEEEEeCCChHHHHHHHhhHHHHHHHHHHHHHHHhhh-h
Confidence 33356666677888889876544332211222211112 33332211 1110000000000000000 001111 1
Q ss_pred cCcCCcc--cCCCccccCcccc---cCCCCC--ccc---cccccccccCCccccCCcEEEEEeccccccceeeehhhHHH
Q 043303 911 PVEDGYH--MGSGEAADTIEAC---CMPPSV--PCS---QLAIESEQIQPRMMSYPVTVIVVNTQNVDKEMIVSRRSTYQ 980 (1639)
Q Consensus 911 P~e~~~~--~~ss~~adE~~~~---~mP~~~--~~~---~~~~~~~~~~g~mls~p~~ViVVNt~~~~k~mI~sRRssYq 980 (1639)
|...... .......+++..+ .++... .+. .++-.. |.-......+|||-++++ |+...
T Consensus 510 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~i~vD~RE~--------~~~~~ 577 (773)
T PRK13766 510 KLQELDEEQKGEEEEKDEQLSLDDFVKSKGKEEEEEEEKEEKDKE----TEEDEPEGPKIIVDSREL--------RSNVA 577 (773)
T ss_pred ccccccccccccccccccccchhhhcccccccccccccccccccc----ccCCCCCCcEEEEeCCCc--------cchhh
Confidence 1100000 0000001111100 000000 000 001100 111123356788888553 22221
Q ss_pred HHHHHhhcCceEEeecCCCCcceeccCceeEEEeecccccccccccccccccchhhHH----HHHHHHHHhhhcccceeE
Q 043303 981 KILALEKEGVQVVERDSDLPVDIIISTATCLVWYDYRNIGKKATALDEASSCLPLCVE----NIATNVLTLLSFTFSVCI 1056 (1639)
Q Consensus 981 ~ILaLEkeG~qVVERd~~LPVDliLS~s~CLvwy~~~~l~~~~~~~~g~sS~lp~~IE----~ia~nvL~aLSfsFs~Ci 1056 (1639)
-.|++.|++|+-|.+.+ =|.+||+.+|. ..|+ ++.++. ...-..+..|+-+|..-+
T Consensus 578 --~~l~~~g~~~~~~~L~~-gDy~~~~~~~v--------ERK~---------~~Dl~~s~~~~r~~~q~~~l~~~~~~~~ 637 (773)
T PRK13766 578 --RHLKRLGAEVELKTLEV-GDYVVSDRVAV--------ERKT---------AEDFVDSIIDRRLFEQVKDLKRAYERPV 637 (773)
T ss_pred --HHHHhCCCEEEEEecCC-CCEEccCCeEE--------EeCc---------HHHHHHHhhcCcHHHHHHHHHhcCCCcE
Confidence 25689999999999999 89999887542 2232 233333 445567889998999999
Q ss_pred EEEeCCchhHHHH--HhhhHHHHHHHhhcCccEEEEEeCCcchhHHHHHHHHhhhhhhcCCC--CCCC-CCCcchhh---
Q 043303 1057 MVFEGDTNFICTV--MESSDGLYAAAASLGLDLQLFCSNSSELTDEIIVSCIGNSIKLTSGL--YPKM-PESETLAE--- 1128 (1639)
Q Consensus 1057 mIFEGe~~Fls~v--L~~~d~LYAAaaslGidlqlfiS~s~e~TdeIIls~I~~~~~~sk~~--~s~m-pESpS~eE--- 1128 (1639)
++.||+......+ -.....|.+.++.+ .+.++.+.++++|+.+| ..++..-.....+ .... ..+.+..|
T Consensus 638 lliE~~~~~~~~~~~~~i~~~l~~l~~~~--~~~ii~~~~~~eta~~l-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 714 (773)
T PRK13766 638 LIIEGDLYTIRNIHPNAIRGALASIAVDF--GIPILFTRDEEETADLL-KVIAKREQEEEKREVSVHGEKKAMTLKEQQE 714 (773)
T ss_pred EEEEcCchhhcccCHHHHHHHHHHHHHHc--CceEEEeCCHHHHHHHH-HHHHhhccccCCCCcccccCCCCCCHHHHHH
Confidence 9999983211110 01112333344444 45678889999999997 5665543211111 1111 12334444
Q ss_pred hhcccCCCCCHHHHHHHHhCCccHHHHHhhchHHHHHHhhccCCChhhHHHHHH
Q 043303 1129 SFLTKFPSVNPLTAHAMLSSKGMLLELLECRHEQRIIAVKKYHVPEESTNLFSI 1182 (1639)
Q Consensus 1129 sfLt~FPsINPLtA~~mLssg~sL~efl~wa~~~qlq~l~~y~VpeeslklF~~ 1182 (1639)
..|...|.|+|-+|..||..=+++..++. +...+++++. .+.++..+.+..
T Consensus 715 ~~L~~ipgig~~~a~~Ll~~fgs~~~i~~-as~~~L~~i~--Gig~~~a~~i~~ 765 (773)
T PRK13766 715 YIVESLPDVGPVLARNLLEHFGSVEAVMT-ASEEELMEVE--GIGEKTAKRIRE 765 (773)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHh-CCHHHHHhCC--CCCHHHHHHHHH
Confidence 25799999999999999999999999988 6667777763 355555555443
No 2
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=98.21 E-value=0.00019 Score=90.19 Aligned_cols=164 Identities=17% Similarity=0.180 Sum_probs=113.6
Q ss_pred HHhhcCceEEeecCCCCcceeccCceeEEEeecccccccccccccccccchhhHHH----HHHHHHHhhhcccceeEEEE
Q 043303 984 ALEKEGVQVVERDSDLPVDIIISTATCLVWYDYRNIGKKATALDEASSCLPLCVEN----IATNVLTLLSFTFSVCIMVF 1059 (1639)
Q Consensus 984 aLEkeG~qVVERd~~LPVDliLS~s~CLvwy~~~~l~~~~~~~~g~sS~lp~~IE~----ia~nvL~aLSfsFs~CimIF 1059 (1639)
.|.+.|++|+=..+.. =|.||||.+|.=.=. ++.+|.+ .+-+++..|+=.|.+-+++-
T Consensus 603 ~L~~~G~~v~p~tL~V-GDYilS~~i~VERKS-----------------i~Dli~Sl~~gRL~~Q~~~m~~~Y~~PvLLI 664 (814)
T TIGR00596 603 LLHRRGIRVIPCMLTV-GDYILTPDICVERKS-----------------ISDLIGSLNNGRLYNQCEKMLRYYAYPVLLI 664 (814)
T ss_pred HHHHCCCEEEEEecCc-ccEEecCCeEEEeCc-----------------HHHHHHHHhcchHHHHHHHHHHhcCCcEEEE
Confidence 5678899999999988 899999988853221 4456554 45677889999999999999
Q ss_pred eCCc--hhH-HH-----HHhhh--HHHHHHHhhcCc---cEEEEEeCCcchhHHHHHHHHhhhhh-hcCCCCCCC-----
Q 043303 1060 EGDT--NFI-CT-----VMESS--DGLYAAAASLGL---DLQLFCSNSSELTDEIIVSCIGNSIK-LTSGLYPKM----- 1120 (1639)
Q Consensus 1060 EGe~--~Fl-s~-----vL~~~--d~LYAAaaslGi---dlqlfiS~s~e~TdeIIls~I~~~~~-~sk~~~s~m----- 1120 (1639)
||+. .|. .. ---+. ..|+.+++.+=+ .|.++.|.+|.+|++|+ .-++.... -.......+
T Consensus 665 E~d~~~~f~l~~~~~~~~~~~~~~~~i~~~L~~L~l~fP~l~IiwS~s~~~TA~i~-~~Lk~~e~epd~~~~v~i~~~~~ 743 (814)
T TIGR00596 665 EFDQNKSFSLEPRNDLSQEISSVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEIF-EELKLGKEEPDPATAAALGSDEN 743 (814)
T ss_pred EecCCcccccccccccccccCccHHHHHHHHHHHHHhcCCceEEecCCHHHHHHHH-HHHHhcCCCCCcccceecCcccc
Confidence 9986 443 00 00011 466666665544 57999999999999998 44444321 111101111
Q ss_pred -----CCCcchhhhhcccCCCCCHHHHHHHHhCCccHHHHHhhchHHHHHHh
Q 043303 1121 -----PESETLAESFLTKFPSVNPLTAHAMLSSKGMLLELLECRHEQRIIAV 1167 (1639)
Q Consensus 1121 -----pESpS~eEsfLt~FPsINPLtA~~mLssg~sL~efl~wa~~~qlq~l 1167 (1639)
+.+-..+--||..+|.|+|-.|..||..=+||.+++. +...+|+++
T Consensus 744 ~~~k~~~~~~~~q~~L~~lPgI~~~~a~~ll~~f~si~~l~~-as~eeL~~~ 794 (814)
T TIGR00596 744 TTAEGLKFNDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAK-LSQNELNEL 794 (814)
T ss_pred cccccccccHHHHHHHHHCCCCCHHHHHHHHHHcCCHHHHHh-CCHHHHHHH
Confidence 1111122345889999999999999999999999999 557777775
No 3
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=93.79 E-value=1.1 Score=51.14 Aligned_cols=182 Identities=23% Similarity=0.324 Sum_probs=123.9
Q ss_pred EEEEEeccccccceeeehhhHHHHHHHHhhcCceEEeecCCCCcceeccCceeEEEeecccccccccccccccccchhhH
Q 043303 958 TVIVVNTQNVDKEMIVSRRSTYQKILALEKEGVQVVERDSDLPVDIIISTATCLVWYDYRNIGKKATALDEASSCLPLCV 1037 (1639)
Q Consensus 958 ~ViVVNt~~~~k~mI~sRRssYq~ILaLEkeG~qVVERd~~LPVDliLS~s~CLvwy~~~~l~~~~~~~~g~sS~lp~~I 1037 (1639)
.++||-++.. .++... -|.+.|+.|.-|-+.+ -|.++|+.+|.= .|+ +..+|
T Consensus 28 ~~viVD~RE~-----rs~v~~-----~L~~~gv~v~~~~Lev-GDYvvs~~v~VE--------RKs---------~~Dfv 79 (254)
T COG1948 28 VVVIVDSREL-----RSEVPR-----LLKRLGVKVEVRTLEV-GDYVVSDDVIVE--------RKS---------ISDFV 79 (254)
T ss_pred eEEEEecchh-----cccchH-----HHHhCCCeEEEEeccc-ccEEeecCeeEE--------ecc---------HHHHH
Confidence 5677777552 222221 3449999999999999 899999977752 222 34555
Q ss_pred HHHH----HHHHHhhhcccceeEEEEeCCchhHHHHHhhhHHHHHHHhhcCcc--EEEEEeCCcchhHHHHHHHHhhhhh
Q 043303 1038 ENIA----TNVLTLLSFTFSVCIMVFEGDTNFICTVMESSDGLYAAAASLGLD--LQLFCSNSSELTDEIIVSCIGNSIK 1111 (1639)
Q Consensus 1038 E~ia----~nvL~aLSfsFs~CimIFEGe~~Fls~vL~~~d~LYAAaaslGid--lqlfiS~s~e~TdeIIls~I~~~~~ 1111 (1639)
.+|. -.+...|.=+|.+=+++.||+..|...---+-+.|+.|.++.-++ +.++.|.++++|+++| ..|+.--.
T Consensus 80 ~Si~dgRlfeQ~~rL~~~y~rpvliVegd~~~~~~~~i~~~av~~al~s~~vdfg~~vi~t~~~~~Ta~~i-~~la~req 158 (254)
T COG1948 80 SSIIDGRLFEQAKRLKKSYERPVLIVEGDDSFSRRPKIHPNAVRGALASLAVDFGLPVIWTRSPEETAELI-HELARREQ 158 (254)
T ss_pred HHHhcchHHHHHHHHHhcCCccEEEEEcccccccccccCHHHHHHHHHHHHhhcCceEEEeCCHHHHHHHH-HHHHHHHH
Confidence 5554 456778999999999999999433322112344455555555554 9999999999999998 55554443
Q ss_pred hcCCC---CCCCCCCcchhh---hhcccCCCCCHHHHHHHHhCCccHHHHHhhchHHHHHHhhc
Q 043303 1112 LTSGL---YPKMPESETLAE---SFLTKFPSVNPLTAHAMLSSKGMLLELLECRHEQRIIAVKK 1169 (1639)
Q Consensus 1112 ~sk~~---~s~mpESpS~eE---sfLt~FPsINPLtA~~mLssg~sL~efl~wa~~~qlq~l~~ 1169 (1639)
..+++ ...++...|..| ..|..+|.|-|..|.-+|..=+|+...+. +.+..|-.+.-
T Consensus 159 ~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~t-as~~eL~~v~g 221 (254)
T COG1948 159 EERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLT-ASEEELMKVKG 221 (254)
T ss_pred HhccccccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhh-cCHHHHHHhcC
Confidence 22222 233444455544 45699999999999999999899888877 66666666654
No 4
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=93.52 E-value=0.51 Score=57.91 Aligned_cols=176 Identities=15% Similarity=0.119 Sum_probs=116.2
Q ss_pred ccceeEEEeecccchhHHH---HHHHHHHHHhhhhccccccccccCcccccccC-cchhhhhhhh--hhccccccccC-C
Q 043303 614 FQQWDVTLYKVKLSDDILA---LIDIFKKSYLAIVHNETELSSFVTSDDFKLLS-LPKQRLMDCI--NRKRFQKANSH-G 686 (1639)
Q Consensus 614 ~~~~~i~lh~V~lSd~I~~---Li~~~~ksYls~l~~~te~~h~~d~d~~kll~-i~K~kL~d~I--~~~~s~~~~~~-~ 686 (1639)
-+.+.|++-+|.+++.|-. ++...-+.+|..|.+--.. ..-+ ++|..|++.. +...+.+- ++ .
T Consensus 205 v~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~~~g~~---------~~~~~~~~kdl~~~~~~~~~~a~~~-~~~~ 274 (542)
T COG1111 205 VKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLKELGVI---------ESSSPVSKKDLLELRQIRLIMAKNE-DSDK 274 (542)
T ss_pred hccceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHcCce---------eccCcccHhHHHHHHHHHHHhccCc-cHHH
Confidence 5778899999999986554 5555567788888776542 2233 6788888776 22222111 11 2
Q ss_pred CCCchhHHHHHHHHhhhhhheeeccchhhhHHhhhhhhccccccchhhhHHHHHhhcc--------ccccc-cCCCCchH
Q 043303 687 DGNCMALITLCSIKLMAWYTCFYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADG--------KIDKE-TSSHPSLL 757 (1639)
Q Consensus 687 ~~~~m~li~L~aiKQaA~ylcfyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~--------kve~~-~~sHPsL~ 757 (1639)
...--.++.+.-+.+|-.||--+||.+.+-|+.++...... ..-+.-++++.+-+. .. .. .=.||||.
T Consensus 275 ~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~--~~sk~a~~l~~d~~~~~al~~~~~~-~~~~v~HPKl~ 351 (542)
T COG1111 275 FRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATK--GGSKAAKSLLADPYFKRALRLLIRA-DESGVEHPKLE 351 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHhcc--cchHHHHHHhcChhhHHHHHHHHHh-ccccCCCccHH
Confidence 22223455666789999999999999999999998765554 223333444322211 11 33 67899999
Q ss_pred HHHHHHhhcccc-CCceEEEEe-chhHHHHHHHHHHhcCCccc-cccC
Q 043303 758 VIQGILQSNSSQ-SNLKVLIVA-EQSFWWSLKCLVMSMGLSCS-ELQN 802 (1639)
Q Consensus 758 ~Iq~iL~s~~~~-~~~K~LIVa-d~~Fwlslk~~L~sMg~s~~-el~~ 802 (1639)
.+..||...... ++.+++|-. =+.-=--+-++|..-|.+.. .|-|
T Consensus 352 ~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiG 399 (542)
T COG1111 352 KLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIG 399 (542)
T ss_pred HHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEee
Confidence 999999999844 467776665 34444567788999888875 5554
No 5
>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3.1.22 from EC) [], and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006259 DNA metabolic process; PDB: 2BHN_D 2BGW_B 1J22_A 1J25_A 1J24_A 1J23_A 2ZIU_A 2ZIW_A 2ZIV_A 2ZIX_A ....
Probab=86.18 E-value=2.5 Score=41.47 Aligned_cols=116 Identities=22% Similarity=0.254 Sum_probs=69.7
Q ss_pred HHHHH-HHhhcCceEEeecCCCCcceeccCceeEEEeeccc----ccccccccccccccchhhHH-HHHHHHHHhhh--c
Q 043303 979 YQKIL-ALEKEGVQVVERDSDLPVDIIISTATCLVWYDYRN----IGKKATALDEASSCLPLCVE-NIATNVLTLLS--F 1050 (1639)
Q Consensus 979 Yq~IL-aLEkeG~qVVERd~~LPVDliLS~s~CLvwy~~~~----l~~~~~~~~g~sS~lp~~IE-~ia~nvL~aLS--f 1050 (1639)
+.+++ +|...|++|+-+.+.+ =|+++.. ...+++... +..|+ ... +-..|. ......+-.|. +
T Consensus 11 ~~~l~~~l~~~gv~~~~~~l~~-gd~~~~~--~~~~~~e~~~~~iverk~--~~d----l~~si~~~rl~~q~~rl~~~~ 81 (143)
T PF02732_consen 11 GEQLLEALRELGVKVEVRQLPV-GDYIWWR--INQISEETMVPVIVERKT--LDD----LVASIKDGRLEEQVQRLKRAS 81 (143)
T ss_dssp HHHHHHHHHCTTSEEEEE--SS-SSEEEEE--S----BESSECEEEEEEE--HHH----HHHHHHTTHHHHHHHHHHCCH
T ss_pred HHHHHHHHHHCCCEEEEEECCC-CCEEEEC--CCCCccccceEEEEEhhH--HHH----HHhhhcCCchHHHHHHHhhcC
Confidence 66777 9999999999997654 5655533 000001110 11111 111 111222 23334444444 7
Q ss_pred ccceeEEEEeCCchhHHHH-----HhhhHHHHHHHhhcCc--cEEEEEeCCcchhHHHHH
Q 043303 1051 TFSVCIMVFEGDTNFICTV-----MESSDGLYAAAASLGL--DLQLFCSNSSELTDEIIV 1103 (1639)
Q Consensus 1051 sFs~CimIFEGe~~Fls~v-----L~~~d~LYAAaaslGi--dlqlfiS~s~e~TdeIIl 1103 (1639)
.|...+++.||...+..+. ..+-..|..+++.+.+ ++.++.+.+.++|++.|.
T Consensus 82 ~~~~~~~lVEg~~~~~~~~~~~~~~~~~~~i~~~L~~lq~~~~~~v~~~~~~~et~~~l~ 141 (143)
T PF02732_consen 82 PFKRVILLVEGLDSYLRKNKNYRRQQSPSAIEEALVELQLRYGISVIFTESWEETADWLA 141 (143)
T ss_dssp CSSEEEEEEESCSSTCCC-----HSSTHHHHHHHHHHHHHCSS-EEEEESSHHHHHHHHH
T ss_pred CCCeEEEEEEccCccccccchhcccCCHHHHHHHHHHHHHHcCeEEEEECCHHHHHHHhh
Confidence 8899899999999887652 2234578888888887 899999999999999973
No 6
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=71.86 E-value=1.1e+02 Score=35.60 Aligned_cols=193 Identities=17% Similarity=0.196 Sum_probs=121.8
Q ss_pred ccCCcEEEEEeccccccceeeehhhHHHHHHHHhhcCceEEeecCCCCcceeccCceeEEEeeccccccccccccccccc
Q 043303 953 MSYPVTVIVVNTQNVDKEMIVSRRSTYQKILALEKEGVQVVERDSDLPVDIIISTATCLVWYDYRNIGKKATALDEASSC 1032 (1639)
Q Consensus 953 ls~p~~ViVVNt~~~~k~mI~sRRssYq~ILaLEkeG~qVVERd~~LPVDliLS~s~CLvwy~~~~l~~~~~~~~g~sS~ 1032 (1639)
..+|.+.||||.++-+-.++.. .+ .+--.=++ |+-.|..|+...|.+.-.-. ++. +
T Consensus 51 ~~~~~~~Ilvn~rQkGNplLk~-----------vr-nv~w~f~d-di~PDf~lg~~~cvLyLSl~------yH~-----l 106 (254)
T KOG2841|consen 51 VTVPGGHILVNPRQKGNPLLKH-----------VR-NVKWEFGD-DIIPDFVLGRGCCVLYLSLK------YHK-----L 106 (254)
T ss_pred CCCCCceEEeccccccChHHHH-----------Hh-cCCeEecC-CCCcceEecCceEEEEeehH------hhh-----c
Confidence 3578899999997744333221 11 12222222 77789999987776654422 111 1
Q ss_pred chhhHHHHHHHHHHhhhcccceeEEEEeCCchhHHHHHhhhHHHHHHHhhcCccEEEEEeCCcchhHHHHHHHHhhhhhh
Q 043303 1033 LPLCVENIATNVLTLLSFTFSVCIMVFEGDTNFICTVMESSDGLYAAAASLGLDLQLFCSNSSELTDEIIVSCIGNSIKL 1112 (1639)
Q Consensus 1033 lp~~IE~ia~nvL~aLSfsFs~CimIFEGe~~Fls~vL~~~d~LYAAaaslGidlqlfiS~s~e~TdeIIls~I~~~~~~ 1112 (1639)
=|.-|-.+ +-.|+=.|..-++++.-+..=...++.-+-.+.-.+ ++-+.++.++|+.+..| ..++...+.
T Consensus 107 ~pdYi~~R----i~~l~k~yk~~VLl~~vd~~e~~~~l~el~k~~~l~-----~~Tl~lA~s~EeaaryI-E~~k~~ek~ 176 (254)
T KOG2841|consen 107 HPDYIYRR----IRKLGKNYKLRVLLVHVDMEEPYKPLLELTKTCDLN-----DVTLVLAWSMEEAARYI-ETYKEYEKK 176 (254)
T ss_pred CcHHHHHH----HHHhcccccceEEEEEecCcchHHHHHHHHHHHHhh-----ceeeeeeccHHHHHHHH-HHHHHhhcC
Confidence 23444333 334556788888888666544455555444444322 67899999999999997 555554433
Q ss_pred cCCCCCCCCCC----cchhhhhcccCCCCCHHHHHHHHhCCccHHHHHhhchHHHHHHhhccCCChhhHHHHHHh
Q 043303 1113 TSGLYPKMPES----ETLAESFLTKFPSVNPLTAHAMLSSKGMLLELLECRHEQRIIAVKKYHVPEESTNLFSIL 1183 (1639)
Q Consensus 1113 sk~~~s~mpES----pS~eEsfLt~FPsINPLtA~~mLssg~sL~efl~wa~~~qlq~l~~y~VpeeslklF~~~ 1183 (1639)
... -.|.-- .+..+.|||.+|+||=--|++||..=|||..++- |-+..|..+.- .=|-|.-++++.|
T Consensus 177 p~d--li~~~~~~d~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~-AS~~ele~~~G-~G~~kak~l~~~l 247 (254)
T KOG2841|consen 177 PID--LIMERKDRDLLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISN-ASEGELEQCPG-LGPAKAKRLHKFL 247 (254)
T ss_pred Cch--hhhhcccccHHHHHHHHHHhCCCCCcccHHHHHHhcccHHHHHh-cCHhHHHhCcC-cCHHHHHHHHHHH
Confidence 321 222111 2358999999999999999999999999999988 77777776653 3345555555544
No 7
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=64.29 E-value=5.5 Score=47.54 Aligned_cols=82 Identities=15% Similarity=0.149 Sum_probs=56.8
Q ss_pred hee-eccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccc-cCCCCchHHHHHHHhhccccCCceEEEEechhHH
Q 043303 706 TCF-YGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKE-TSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFW 783 (1639)
Q Consensus 706 lcf-yGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~-~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fw 783 (1639)
+.+ ||++...-+|+.+++-++....+ +...++++..+.... .+.|+.| .|.|+.|++|...-
T Consensus 239 ~~~P~G~~~T~~~L~~la~~~g~~~~~---~~~~~~~er~~~~~~l~~~~~~l-------------~Gkrvai~g~~~~~ 302 (427)
T PRK02842 239 APFPLGPEGTRAWLEAAAAAFGIDPDG---LEEREAPAWERARKALEPYRELL-------------RGKRVFFLPDSQLE 302 (427)
T ss_pred CCCCcChHHHHHHHHHHHHHhCcCHhH---HHHHHHHHHHHHHHHHHHhhhhc-------------CCcEEEEECCchhH
Confidence 445 99999999999999777643221 233444444443333 2333322 37899999999999
Q ss_pred HHHHHHHHh-cCCccccccCc
Q 043303 784 WSLKCLVMS-MGLSCSELQNF 803 (1639)
Q Consensus 784 lslk~~L~s-Mg~s~~el~~~ 803 (1639)
+++.++|.. |||..+....+
T Consensus 303 ~~la~~L~eelGm~~v~v~t~ 323 (427)
T PRK02842 303 IPLARFLSRECGMELVEVGTP 323 (427)
T ss_pred HHHHHHHHHhCCCEEEEeCCC
Confidence 999999999 99998766654
No 8
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=57.52 E-value=1.4e+02 Score=39.80 Aligned_cols=164 Identities=17% Similarity=0.180 Sum_probs=109.8
Q ss_pred HHhhcCceEEeecCCCCcceeccCceeEEEeecccccccccccccccccchhhHH----HHHHHHHHhhhcccceeEEEE
Q 043303 984 ALEKEGVQVVERDSDLPVDIIISTATCLVWYDYRNIGKKATALDEASSCLPLCVE----NIATNVLTLLSFTFSVCIMVF 1059 (1639)
Q Consensus 984 aLEkeG~qVVERd~~LPVDliLS~s~CLvwy~~~~l~~~~~~~~g~sS~lp~~IE----~ia~nvL~aLSfsFs~CimIF 1059 (1639)
.|-+.|++|+==-+-. =|.||||.+|.=- |+ ++.-|. ..+-++...|+-.|.+-+++.
T Consensus 669 ~Lh~~G~~Vip~tL~v-GDYIlSP~icVER--------KS---------IsDLi~SLnsgRly~Q~~~M~~~Y~~pvLLI 730 (892)
T KOG0442|consen 669 LLHRKGLRVIPCTLEV-GDYILSPDICVER--------KS---------ISDLIQSLNSGRLYNQCEMMQRYYERPVLLI 730 (892)
T ss_pred HHHhCCceEEEEeecc-cCEEccccceeee--------cc---------HHHHHHhhhcchHHHHHHHHHHhccCcEEEE
Confidence 4567899999888777 7999999999632 22 222232 345555556666676666655
Q ss_pred eCC--chhH---------HHHHhhhHHHHHHHhhcCccEEEEEeCCcchhHHHHHHHHhhhh---hhcCCCCCCCC-CCc
Q 043303 1060 EGD--TNFI---------CTVMESSDGLYAAAASLGLDLQLFCSNSSELTDEIIVSCIGNSI---KLTSGLYPKMP-ESE 1124 (1639)
Q Consensus 1060 EGe--~~Fl---------s~vL~~~d~LYAAaaslGidlqlfiS~s~e~TdeIIls~I~~~~---~~sk~~~s~mp-ESp 1124 (1639)
|-+ ..|- ....+......+.+.--+=.+.|+.|++|..|++|+ .-++-.- .-+. ..-++ +++
T Consensus 731 Efd~~k~fs~~~~~~ls~e~sk~~i~skL~lLil~fP~LRilWS~Sp~~Ta~if-~eLKl~~~epD~~~--Ai~lg~~~~ 807 (892)
T KOG0442|consen 731 EFDQEKSFSLQPRSDLSQELSKNDIVSKLTLLILAFPKLRILWSSSPLATAEIF-EELKLSEPEPDPAR--AISLGTDEE 807 (892)
T ss_pred EecCCCCcCCCCccchhhhhhHHHHHHHHHHHHhcCCceEEEecCchhHHHHHH-HHHhhcCCCCCcch--heeeccccc
Confidence 443 3332 355555677777777777789999999999999998 4333221 1001 11111 122
Q ss_pred chhh---------hhcccCCCCCHHHHHHHHhCCccHHHHHhhchHHHHHHhhc
Q 043303 1125 TLAE---------SFLTKFPSVNPLTAHAMLSSKGMLLELLECRHEQRIIAVKK 1169 (1639)
Q Consensus 1125 S~eE---------sfLt~FPsINPLtA~~mLssg~sL~efl~wa~~~qlq~l~~ 1169 (1639)
+-.| =||..-|.|+=..++-|..+..||.++.. ...+.|.+|..
T Consensus 808 ~~~~~~~~n~~~~~fll~lPgVs~~n~~~l~~k~ks~~~La~-sS~~el~el~~ 860 (892)
T KOG0442|consen 808 GNSESESYNSSALDFLLSLPGVSYINYRNLRHKFKSLKELAN-SSQEELSELLG 860 (892)
T ss_pred ccccccccCchHHHHHhcCCCccHHHHHHHHHHhhHHHHHHh-CcHHHHHHHhc
Confidence 2222 37899999999999999999999998777 66777887776
No 9
>TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme involved in bacteriochlorophyll biosynthesis. This subunit shows homology to the nitrogenase molybdenum-iron protein NifN.
Probab=51.44 E-value=9.8 Score=45.26 Aligned_cols=76 Identities=9% Similarity=0.161 Sum_probs=51.6
Q ss_pred eccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhHHHHHHH
Q 043303 709 YGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWSLKC 788 (1639)
Q Consensus 709 yGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwlslk~ 788 (1639)
||++...-+|+++++-++..+.. ++++..+. ...+........|.|+.|++|...=+++.+
T Consensus 231 iGi~~T~~~l~~la~~~g~~~~~-------~~~e~~~~------------~~~l~~~~~~l~Gkrv~i~gd~~~~~~l~~ 291 (407)
T TIGR01279 231 FGPDGTRRFLEAIAAEFGIEVDK-------LSEREAQA------------WRALEPHTQLLRGKKIFFFGDNLLELPLAR 291 (407)
T ss_pred cCHHHHHHHHHHHHHHhCcCHHH-------HHHHHHHH------------HHHHHHHHHhcCCCEEEEECCchHHHHHHH
Confidence 99999999999999877755432 22222111 111111111124889999999999999999
Q ss_pred HHHhcCCccccccCc
Q 043303 789 LVMSMGLSCSELQNF 803 (1639)
Q Consensus 789 ~L~sMg~s~~el~~~ 803 (1639)
+|..|||..+....+
T Consensus 292 ~L~elGm~~v~~~t~ 306 (407)
T TIGR01279 292 FLKRCGMEVVECGTP 306 (407)
T ss_pred HHHHCCCEEEEecCC
Confidence 999999997765543
No 10
>cd01979 Pchlide_reductase_N Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=50.31 E-value=12 Score=44.07 Aligned_cols=75 Identities=12% Similarity=0.226 Sum_probs=52.7
Q ss_pred eccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccc-cCCCCchHHHHHHHhhccccCCceEEEEechhHHHHHH
Q 043303 709 YGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKE-TSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWSLK 787 (1639)
Q Consensus 709 yGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~-~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwlslk 787 (1639)
||++...-+|+++++-++..++ .|+++..+.... .+.|+.| .|.|+.|++|...=+++.
T Consensus 233 ~G~~~t~~~l~~la~~~g~~~~-------~i~~e~~~~~~~l~~~~~~l-------------~Gkrv~i~g~~~~~~~la 292 (396)
T cd01979 233 IGPDGTRAWLEAICSAFGIFPS-------VLAEREARAWRALEPYLDLL-------------RGKSIFFMGDNLLEIPLA 292 (396)
T ss_pred cChHHHHHHHHHHHHHhCCChh-------HHHHHHHHHHHHHHHHHHhh-------------cCCEEEEECCchHHHHHH
Confidence 8999999999999977764432 344443333222 2223322 378999999999999999
Q ss_pred HHHHhcCCccccccCc
Q 043303 788 CLVMSMGLSCSELQNF 803 (1639)
Q Consensus 788 ~~L~sMg~s~~el~~~ 803 (1639)
++|..|||..+....+
T Consensus 293 ~~L~elGm~vv~~~t~ 308 (396)
T cd01979 293 RFLTRCGMIVVEVGTP 308 (396)
T ss_pred HHHHHCCCEEEeeCCC
Confidence 9999999998876554
No 11
>COG2710 NifD Nitrogenase molybdenum-iron protein, alpha and beta chains [Energy production and conversion]
Probab=34.90 E-value=35 Score=41.65 Aligned_cols=89 Identities=22% Similarity=0.249 Sum_probs=60.9
Q ss_pred HHHH--HHHhhhhhh------------eeeccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccC-CCCchHH
Q 043303 694 ITLC--SIKLMAWYT------------CFYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETS-SHPSLLV 758 (1639)
Q Consensus 694 i~L~--aiKQaA~yl------------cfyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~-sHPsL~~ 758 (1639)
++|| +.+.+|.|| -+||+-..-.+|++++.-+.. -+..-..++.+....++..++ .|+-+.
T Consensus 237 l~lc~~~~~~~a~~~~~~~gip~~~~~~~~G~~~t~~~l~~la~~~g~---~~~~~e~v~~e~~~l~d~~~d~~~~~l~- 312 (456)
T COG2710 237 LVLCSRSGRYLARYLEERFGIPWIEVPSPLGIENTDRFLRNLAKLLGK---IEEIPEEVIEERGALIDAELDRYRPRLS- 312 (456)
T ss_pred hhhhhHHHHHHHHHHHHHhCCCeEecCCCcCchHHHHHHHHHHHHhCC---cccccHHHHHHHHHHHHHHHHHHHHHhc-
Confidence 4554 788888887 689999999999999876664 111122333333333333333 444332
Q ss_pred HHHHHhhccccCCceEEEEechhHHHHHHHHHHhcCCccc
Q 043303 759 IQGILQSNSSQSNLKVLIVAEQSFWWSLKCLVMSMGLSCS 798 (1639)
Q Consensus 759 Iq~iL~s~~~~~~~K~LIVad~~Fwlslk~~L~sMg~s~~ 798 (1639)
|.|+.|.++--.|..+..+...|||.-+
T Consensus 313 ------------gk~v~I~~~~~~~~~~~~~~~elgm~~v 340 (456)
T COG2710 313 ------------GKKVAIYGGPDAIHLLAAFEEELGMEPV 340 (456)
T ss_pred ------------CCEEEEEeCCcchHHHHHHHHHcCCEEE
Confidence 7999999976999999999999999944
No 12
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.29 E-value=70 Score=31.05 Aligned_cols=59 Identities=20% Similarity=0.115 Sum_probs=42.0
Q ss_pred eEEEEe-chhHHHHHHHHHHhcCCccccccCcccccCCccccccccccccccccCCCcceeeecccccc
Q 043303 773 KVLIVA-EQSFWWSLKCLVMSMGLSCSELQNFYTHVDQPDVTKVYGSASAKMTDLPISDCLMVSHESVS 840 (1639)
Q Consensus 773 K~LIVa-d~~Fwlslk~~L~sMg~s~~el~~~~~s~~~~D~~e~~~f~~~~~~~L~~SDCLL~s~~hI~ 840 (1639)
+||||+ ..-.+-.+++.+...|..+..+ ++...... .+......+..+||+|+.-+.|+
T Consensus 1 ~vliVGG~~~~~~~~~~~~~~~G~~~~~h-g~~~~~~~--------~~~~l~~~i~~aD~VIv~t~~vs 60 (97)
T PF10087_consen 1 SVLIVGGREDRERRYKRILEKYGGKLIHH-GRDGGDEK--------KASRLPSKIKKADLVIVFTDYVS 60 (97)
T ss_pred CEEEEcCCcccHHHHHHHHHHcCCEEEEE-ecCCCCcc--------chhHHHHhcCCCCEEEEEeCCcC
Confidence 589999 5889999999999999998888 32110000 01113446778999999888776
No 13
>PRK14478 nitrogenase molybdenum-cofactor biosynthesis protein NifE; Provisional
Probab=26.32 E-value=42 Score=41.14 Aligned_cols=85 Identities=13% Similarity=0.190 Sum_probs=56.2
Q ss_pred heeeccchhhhHHhhhhhhcc--cccc-chhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhH
Q 043303 706 TCFYGIHTARLCVDKLCKSQG--CLKS-RLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSF 782 (1639)
Q Consensus 706 lcfyGIH~Ahlyl~~l~~s~e--~~~~-~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~F 782 (1639)
..+||++...-+|+.+++-+. ..+. ........|+++.++.... ++.+...+ .|.|+.|.++...
T Consensus 268 ~~p~G~~~T~~~l~~la~~~~~~~~~~~~~~~~e~~i~~e~~~~~~~---------l~~~~~~l---~Gk~vaI~~~~~~ 335 (475)
T PRK14478 268 GSFYGIEDTSDSLRQIARLLVERGADAELVERTEALIAEEEAKAWAA---------LEPYRPRL---EGKRVLLYTGGVK 335 (475)
T ss_pred cCCCcHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHHH---------HHHHHHHh---CCCEEEEEcCCch
Confidence 357999999999999998872 2232 3334555676666555333 22322222 3788887776655
Q ss_pred HHHHHHHHHhcCCccccccC
Q 043303 783 WWSLKCLVMSMGLSCSELQN 802 (1639)
Q Consensus 783 wlslk~~L~sMg~s~~el~~ 802 (1639)
=+++-++|..|||.......
T Consensus 336 ~~~la~~l~ElGm~v~~~~~ 355 (475)
T PRK14478 336 SWSVVKALQELGMEVVGTSV 355 (475)
T ss_pred HHHHHHHHHHCCCEEEEEEE
Confidence 66888899999999775544
No 14
>cd03466 Nitrogenase_NifN_2 Nitrogenase_nifN_2: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). This group also contains the Clostidium fused NifN-NifB protein.
Probab=25.44 E-value=1.1e+02 Score=36.97 Aligned_cols=72 Identities=15% Similarity=0.227 Sum_probs=49.5
Q ss_pred eccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhHHHHHHH
Q 043303 709 YGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWSLKC 788 (1639)
Q Consensus 709 yGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwlslk~ 788 (1639)
||++...-+|+.+++-++... ...|++++.+ .++.++.......+.|+.|+++....+++.+
T Consensus 256 ~G~~~t~~~l~~l~~~~g~~~------~~~i~~~~~~------------~~~~~~d~~~~l~gkrv~v~g~~~~~~~l~~ 317 (429)
T cd03466 256 IGLRATDEFMSLLSKLTGKPI------PEKYTRERGR------------LLDAMIDAHKYNFGRKAAIYGEPDFVVAITR 317 (429)
T ss_pred cChHHHHHHHHHHHHHHCCCc------CHHHHHHHHH------------HHHHHHHHHHhcCCCEEEEEcCHHHHHHHHH
Confidence 899999999999887665321 1123222211 2333444333446899999999999999999
Q ss_pred HHHhcCCccc
Q 043303 789 LVMSMGLSCS 798 (1639)
Q Consensus 789 ~L~sMg~s~~ 798 (1639)
+|..|||..+
T Consensus 318 ~L~elG~~~~ 327 (429)
T cd03466 318 FVLENGMVPV 327 (429)
T ss_pred HHHHCCCEEE
Confidence 9999999854
No 15
>cd01974 Nitrogenase_MoFe_beta Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems. Mo-nitrogenase consists of the MoFe protein (component 1) and the Fe protein (component 2). MoFe is an alpha2beta2 tetramer. This group contains the beta subunit of the MoFe protein. Each alphabeta pair of MoFe contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein contains a single [4Fe-4S] cluster. Electrons are transferred from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe and in turn to FeMoCo, the site of substrate reduction.
Probab=25.01 E-value=41 Score=40.44 Aligned_cols=78 Identities=12% Similarity=0.207 Sum_probs=51.5
Q ss_pred eeeccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhHHHHH
Q 043303 707 CFYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWSL 786 (1639)
Q Consensus 707 cfyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwlsl 786 (1639)
-.||++...-+|+.+++-++... -..|++++.+. ++.+........+.|+.|.+|....+++
T Consensus 257 ~p~G~~~t~~~l~~l~~~~g~~~------~~~i~~er~~~------------~~~~~~~~~~l~gkrv~i~g~~~~~~~l 318 (435)
T cd01974 257 MPIGVAATDEFLMALSELTGKPI------PEELEEERGRL------------VDAMTDSHQYLHGKKFALYGDPDFLIGL 318 (435)
T ss_pred CCcChHHHHHHHHHHHHHhCCCC------CHHHHHHHHHH------------HHHHHHHHHhcCCCEEEEEcChHHHHHH
Confidence 37899999999999887665421 11233333322 2222222222347888888899999999
Q ss_pred HHHHHhcCCccccccC
Q 043303 787 KCLVMSMGLSCSELQN 802 (1639)
Q Consensus 787 k~~L~sMg~s~~el~~ 802 (1639)
.++|..|||..+....
T Consensus 319 a~~L~elGm~v~~~~~ 334 (435)
T cd01974 319 TSFLLELGMEPVHVLT 334 (435)
T ss_pred HHHHHHCCCEEEEEEe
Confidence 9999999999865543
No 16
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=24.06 E-value=1.3e+02 Score=37.57 Aligned_cols=85 Identities=7% Similarity=0.103 Sum_probs=53.9
Q ss_pred eeeccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhHHHHH
Q 043303 707 CFYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWSL 786 (1639)
Q Consensus 707 cfyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwlsl 786 (1639)
..+|++..--+|+.+++-++..+... ...|++..... ..+..+.+.+.. ....+.|+.|++|...++++
T Consensus 240 ~PiG~~~T~~fL~~la~~~g~~~~~~---e~~i~~~~~~~-------~~l~~~~~~~d~-~~l~Gkrv~I~gd~~~a~~l 308 (519)
T PRK02910 240 VPIGVGATARFIREVAELLNLDGADL---EAFILDGLSAP-------SRLPWFSRSVDS-TYLTGKRVFVFGDATHAVAA 308 (519)
T ss_pred ccccHHHHHHHHHHHHHHhCCChhhh---HHHHHHHHhhh-------hhhhHHHHhhhh-HhhcCCEEEEEcCcHHHHHH
Confidence 57899999999999887665432211 12222221111 112223333333 22347899999999999999
Q ss_pred HHHHH-hcCCccccccC
Q 043303 787 KCLVM-SMGLSCSELQN 802 (1639)
Q Consensus 787 k~~L~-sMg~s~~el~~ 802 (1639)
.++|. .|||.++..+.
T Consensus 309 ~~~L~~ElGm~vv~~gt 325 (519)
T PRK02910 309 ARILSDELGFEVVGAGT 325 (519)
T ss_pred HHHHHHhcCCeEEEEec
Confidence 99999 79999886544
No 17
>TIGR01282 nifD nitrogenase molybdenum-iron protein alpha chain. Nitrogenase consists of alpha (NifD) and beta (NifK) subunits of the molybdenum-iron protein and an ATP-binding iron-sulfur protein (NifH). This model describes a large clade of NifD proteins, but excludes a lineage that contains putative NifD and NifD homologs from species with vanadium-dependent nitrogenases.
Probab=23.30 E-value=51 Score=40.44 Aligned_cols=79 Identities=11% Similarity=0.129 Sum_probs=51.1
Q ss_pred eeeccchhhhHHhhhhhhccc-cccchhhhHHHHHhhccccccccC-CCCchHHHHHHHhhccccCCceEEEEechhHHH
Q 043303 707 CFYGIHTARLCVDKLCKSQGC-LKSRLGSLQSLVVAADGKIDKETS-SHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWW 784 (1639)
Q Consensus 707 cfyGIH~Ahlyl~~l~~s~e~-~~~~L~~i~slI~~a~~kve~~~~-sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwl 784 (1639)
.|||+....-+|+++++-++. ++++ +..+|+++...++.-++ .|+.|. |.|+.|.++..-=+
T Consensus 285 ~~~Gi~~T~~~Lr~ia~~~g~~i~~~---~e~~I~~e~~~~~~~ld~~~~~L~-------------GKrv~i~~g~~~~~ 348 (466)
T TIGR01282 285 NFFGPTKIAESLRKIAEFFDDEIKEK---AEEVIAKYQPAVDAVIAKYRPRLE-------------GKTVMLYVGGLRPR 348 (466)
T ss_pred CCCCHHHHHHHHHHHHHHHCchhHHH---HHHHHHHHHHHHHHHHHHHHHhcC-------------CCEEEEECCCCcHH
Confidence 479999999999999988863 3443 33556666665544433 444333 78888887322222
Q ss_pred HHHHHHHhcCCcccccc
Q 043303 785 SLKCLVMSMGLSCSELQ 801 (1639)
Q Consensus 785 slk~~L~sMg~s~~el~ 801 (1639)
++-.+|..|||..+-.+
T Consensus 349 ~~~~~l~ELGmevv~~g 365 (466)
T TIGR01282 349 HVIGAFEDLGMEVIGTG 365 (466)
T ss_pred HHHHHHHHCCCEEEEEe
Confidence 23336889999987443
No 18
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=22.77 E-value=1.2e+02 Score=37.62 Aligned_cols=87 Identities=7% Similarity=0.135 Sum_probs=50.7
Q ss_pred eeeccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhHHHHH
Q 043303 707 CFYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWSL 786 (1639)
Q Consensus 707 cfyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwlsl 786 (1639)
-.+|++..--+|+++++-++.....- .....|++......+ .......+.... ..+.|+.|++|....+++
T Consensus 240 ~PiG~~~T~~fL~~l~~~~~~~g~~~-~~e~~i~~e~~~~~~-------~~~~~r~~d~~~-l~Gkrv~I~gd~~~a~~l 310 (511)
T TIGR01278 240 TPIGVNATRRFIREIAALLNQAGADP-YYESFILDGLSAVSQ-------AAWFARSIDSQS-LTGKRAFVFGDATHAVGM 310 (511)
T ss_pred cccCHHHHHHHHHHHHHHHhhcCCCC-cHHHHHHhhhhhhhh-------HHHHHhhhhhHH-hcCCeEEEEcCcHHHHHH
Confidence 78899999999999886652111000 011222222111100 111111222222 347899999999999999
Q ss_pred HHHHH-hcCCccccccC
Q 043303 787 KCLVM-SMGLSCSELQN 802 (1639)
Q Consensus 787 k~~L~-sMg~s~~el~~ 802 (1639)
.++|. .|||.++-.+.
T Consensus 311 ~~~L~~ElG~~vv~~gt 327 (511)
T TIGR01278 311 TKILARELGIHIVGAGT 327 (511)
T ss_pred HHHHHHhCCCEEEecCC
Confidence 99998 89999875443
No 19
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=22.20 E-value=45 Score=41.24 Aligned_cols=78 Identities=17% Similarity=0.225 Sum_probs=53.9
Q ss_pred eeccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhHHHHHH
Q 043303 708 FYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWSLK 787 (1639)
Q Consensus 708 fyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwlslk 787 (1639)
.||+...--+|+++++-++..++. |+++..+.-.. +...+.+| .|.|+.+++|...=++|-
T Consensus 270 PiGi~~Td~fLr~Ia~~~G~~pe~-------l~~Er~rl~da------l~d~~~~L------~GKrvai~Gdp~~~i~La 330 (457)
T CHL00073 270 PIGPDGTRAWIEKICSVFGIEPQG-------LEEREEQIWES------LKDYLDLV------RGKSVFFMGDNLLEISLA 330 (457)
T ss_pred cCcHHHHHHHHHHHHHHhCcCHHH-------HHHHHHHHHHH------HHHHHHHH------CCCEEEEECCCcHHHHHH
Confidence 489999999999999877743322 33333333222 22222233 389999888988999999
Q ss_pred HHHHhcCCccccccCcc
Q 043303 788 CLVMSMGLSCSELQNFY 804 (1639)
Q Consensus 788 ~~L~sMg~s~~el~~~~ 804 (1639)
++|..|||..+..+.+.
T Consensus 331 rfL~elGmevV~vgt~~ 347 (457)
T CHL00073 331 RFLIRCGMIVYEIGIPY 347 (457)
T ss_pred HHHHHCCCEEEEEEeCC
Confidence 99999999988775553
No 20
>cd01973 Nitrogenase_VFe_beta_like Nitrogenase_VFe_beta -like: Nitrogenase VFe protein, beta subunit like. This group contains proteins similar to the beta subunits of the VFe protein of the vanadium-dependent (V-) nitrogenase. Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V-nitrogenase there is a molybdenum (Mo)-dependent nitrogenase and an iron only (Fe-) nitrogenase. The Mo-nitrogenase is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe p
Probab=21.68 E-value=75 Score=38.94 Aligned_cols=75 Identities=15% Similarity=0.162 Sum_probs=48.4
Q ss_pred eeeccchhhhHHhhhhhhccccccchhhhHHHHHhhccccccccCCCCchHHHHHHHh-hccccCCceEEEEechhHHHH
Q 043303 707 CFYGIHTARLCVDKLCKSQGCLKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQ-SNSSQSNLKVLIVAEQSFWWS 785 (1639)
Q Consensus 707 cfyGIH~Ahlyl~~l~~s~e~~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~-s~~~~~~~K~LIVad~~Fwls 785 (1639)
-+||++..--+|+++++-++.-. ...|.+++. ..+..++. .-....|.|+.|++|....++
T Consensus 258 ~P~G~~~T~~~l~~ia~~~g~~~------~e~i~~er~------------~~~~~~~~~~~~~l~Gkrv~i~g~~~~~~~ 319 (454)
T cd01973 258 TPIGIKNTDAFLQNIKELTGKPI------PESLVRERG------------IAIDALADLAHMFFANKKVAIFGHPDLVIG 319 (454)
T ss_pred CCcChHHHHHHHHHHHHHHCCCC------CHHHHHHHH------------HHHHHHHHHHHHHhCCCeEEEEcCHHHHHH
Confidence 37899999999999987665321 112222211 12222222 111124888988889999999
Q ss_pred HHHHHHhcCCcccc
Q 043303 786 LKCLVMSMGLSCSE 799 (1639)
Q Consensus 786 lk~~L~sMg~s~~e 799 (1639)
+.++|..|||..+-
T Consensus 320 l~~fl~elGm~~~~ 333 (454)
T cd01973 320 LAEFCLEVEMKPVL 333 (454)
T ss_pred HHHHHHHCCCeEEE
Confidence 99999999999654
No 21
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain. This model represents the majority of known sequences of the nitrogenase molybdenum-iron protein beta subunit. A distinct clade in a phylogenetic tree contains molybdenum-iron, vanadium-iron, and iron-iron forms of nitrogenase beta subunit and is excluded from this model. Nitrogenase, also called dinitrogenase, is responsible for nitrogen fixation. Note: the trusted cutoff score has recently been lowered to include an additional family in which the beta subunit is shorter by about 50 amino acids at the N-terminus. In species with the shorter form of the beta subunit, the alpha subunit has a novel insert of similar length.
Probab=21.58 E-value=49 Score=41.30 Aligned_cols=76 Identities=13% Similarity=0.228 Sum_probs=49.9
Q ss_pred eeeccchhhhHHhhhhhhccc-cccchhhhHHHHHhhccccccccCCCCchHHHHHHHhhccccCCceEEEEechhHHHH
Q 043303 707 CFYGIHTARLCVDKLCKSQGC-LKSRLGSLQSLVVAADGKIDKETSSHPSLLVIQGILQSNSSQSNLKVLIVAEQSFWWS 785 (1639)
Q Consensus 707 cfyGIH~Ahlyl~~l~~s~e~-~~~~L~~i~slI~~a~~kve~~~~sHPsL~~Iq~iL~s~~~~~~~K~LIVad~~Fwls 785 (1639)
.-+|++..--+|.++++-++. .|. .|+.+++. .+..+..+.....|.|+.|.+|..+.++
T Consensus 317 ~PiGi~~Td~fL~~la~~~g~~ip~-------~i~~eR~r------------l~dam~d~~~~l~GKrvaI~gdpd~~~~ 377 (515)
T TIGR01286 317 IPLGVKGTDEFLMKVSEISGQPIPA-------ELTKERGR------------LVDAMTDSHAWLHGKRFAIYGDPDFVMG 377 (515)
T ss_pred CCccHHHHHHHHHHHHHHHCCCCCH-------HHHHHHHH------------HHHHHHHHHHHhcCceEEEECCHHHHHH
Confidence 358888888899998876664 222 23332222 1222222222234789988899999999
Q ss_pred HHHHHHhcCCcccccc
Q 043303 786 LKCLVMSMGLSCSELQ 801 (1639)
Q Consensus 786 lk~~L~sMg~s~~el~ 801 (1639)
+.++|..|||..+...
T Consensus 378 l~~fL~ElGmepv~v~ 393 (515)
T TIGR01286 378 LVRFVLELGCEPVHIL 393 (515)
T ss_pred HHHHHHHCCCEEEEEE
Confidence 9999999999965443
Done!