Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate GFF1685 PGA1_c17080 pyruvate ferredoxin/flavodoxin oxidoreductase-like protein
Query= reanno::Cup4G11:RR42_RS19540 (1197 letters) >FitnessBrowser__Phaeo:GFF1685 Length = 1139 Score = 1031 bits (2665), Expect = 0.0 Identities = 557/1178 (47%), Positives = 758/1178 (64%), Gaps = 46/1178 (3%) Query: 20 VSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLW 79 +SL DK+ L + +V ++GTQALVRL ++Q+ RD+AAGLNTAG ++GYRGSPLGA+D + Sbjct: 6 ISLNDKFDLTKSQVMLNGTQALVRLMLMQKHRDKAAGLNTAGLVTGYRGSPLGAVDMQMK 65 Query: 80 KAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDV 139 +A++HL A D+ FQ GLNEDLA T++WG+QQ + + +++GVFG+WYGKGPGVDR+ D Sbjct: 66 RAEKHLTASDVTFQFGLNEDLAVTALWGAQQAEVRGEGKYDGVFGLWYGKGPGVDRSGDA 125 Query: 140 FKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLH 199 +HAN AGSS+HGGVLV GDDH +SST+ HQSE C LP++ P+ VQE LDYG + Sbjct: 126 IRHANMAGSSKHGGVLVAMGDDHTGESSTVLHQSEWSLMDCYLPIVSPAGVQEILDYGAY 185 Query: 200 AWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPLEQ 259 A+SR+SGLWV +K + D +E ++ V+ DP R+++V P +F +P GLNIR D Q Sbjct: 186 GLALSRFSGLWVGLKTMKDTIEVTSVVDGDPDRMKLVTP-EFDMPADGLNIRLDDDRFRQ 244 Query: 260 EARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCA 319 E R++DYK +A A+ ANK+D+ P A+ G + GK +LD A++ L +D+ Sbjct: 245 ENRIIDYKRFAAEAFSHANKMDKRMWGKPGAKIGFVAAGKNWLDLVHAMSLLNIDETMAE 304 Query: 320 RIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVY 379 R+GI YKVG WPL+ G +AEGL I+VVEEKR+++E +KE +++ R R VY Sbjct: 305 RLGITTYKVGQTWPLDMKGFNDWAEGLDLIVVVEEKRKLIEIQIKEAIFDDRQGRR--VY 362 Query: 380 GKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAARIAV 439 G + GG ++ + L P Y L P +IA + L E + A I A + Sbjct: 363 GWY-----KGGAGAMHREE-LFPTKYALDPIMIAEKLGQIL--IEEGRETEA-IRAGLTA 413 Query: 440 IEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTSTFS 499 ++ ++A +AA R P+FCSGCPHN+ST +P+GSRA AGIGCH+M WMDR T+ F+ Sbjct: 414 LDDAKRADNAEEIAA-RLPYFCSGCPHNSSTKLPDGSRAYAGIGCHFMVQWMDRETTGFT 472 Query: 500 QMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAVAM 559 MGGEGV W+G+APF+ KHVF NLGDGTY HSG+ AIRA++A G NIT+KILYNDAVAM Sbjct: 473 HMGGEGVNWVGEAPFSNRKHVFQNLGDGTYNHSGVQAIRAALAEGTNITFKILYNDAVAM 532 Query: 560 TGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRIQR 619 TGGQ +G L+ +A+++ A G + I VV DE E A + P G+ +H R EL +Q+ Sbjct: 533 TGGQEAEGGLTAHQIAHELTAMGMKTIAVVYDEKEDVDAKL-FPAGMRMHERAELMAVQK 591 Query: 620 ELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLSVE 679 E+ V G + +IY QTCA EKRRRRK+G +PDP +R FIN VCEGCGDC V+SNC+S+ Sbjct: 592 EMETVEGVSAIIYIQTCAAEKRRRRKKGLFPDPDQRVFINSDVCEGCGDCGVQSNCVSIV 651 Query: 680 PLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPALPQPAL 739 P ETELG KR I+QSSCNKDFSCV GFCPSF+T EGA+++K + +LP LP+P L Sbjct: 652 PKETELGRKRAIDQSSCNKDFSCVKGFCPSFLTIEGAKIRKEPTAAL---DLPDLPKPEL 708 Query: 740 PGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQIAA 799 P + + V++TGVGGTGVVTIG +L AA ++ KG +++MAGLAQKGGAV H +IA Sbjct: 709 PSINGTHNVVITGVGGTGVVTIGAVLAQAAQIDGKGAGMMEMAGLAQKGGAVHIHCRIAN 768 Query: 800 HPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFIKNPKW 859 P+ + A R+A GEA +IG D +VSA I + G+T A+VN+ + T +F ++ + Sbjct: 769 KPEDISAIRVATGEAHALIGGDLVVSAGAKTIGLMKTGKTGAVVNSHEIITGDFTRDTDF 828 Query: 860 QFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLSLDALV 919 Q P + + + + D +AS LA A +GD+IF+N ++ G AWQ+G LP+SL+A+ Sbjct: 829 QLPTDRLQVALEARLRDRLDLFDASDLARASMGDSIFSNMMIFGAAWQRGLLPISLEAIQ 888 Query: 920 RAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGALLEKL 979 AI LNG AVE+N AFD GR P+ V L VV+LP S LE+ Sbjct: 889 EAITLNGAAVERNLRAFDIGRWAVLYPQEVQKLI--------APNVVELPKS----LEEQ 936 Query: 980 IAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLMAYKDE 1039 IA R+ L YQ A+ + + + A+ A L E+ A+ KL++YKDE Sbjct: 937 IAFRSAQLVDYQGPRLAKRYGKMLDGI--ADKA---------LKESVAKGYHKLLSYKDE 985 Query: 1040 YEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMKL 1099 YEVARL +K +FEG D ++++ LAPP++ +D G KR+FGP + Sbjct: 986 YEVARLLLSS--REKAEAEFEG----DLKISYNLAPPMLTGKDPDGRPKKRKFGPGLERG 1039 Query: 1100 FGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAITLASLP 1159 +LAK KGLRG DVFG TAER+ ERALI +Y A ++E S A I LA LP Sbjct: 1040 LRLLAKFKGLRGTPLDVFGYTAERKMERALIAQYEADMKEWLPKASPEIMAPLIALAELP 1099 Query: 1160 DDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQRVA 1197 +IRGFG VK N +K R LL RH T + A Sbjct: 1100 LEIRGFGPVKQANESKAAKRREELLAALRHGGTELKTA 1137 Lambda K H 0.319 0.135 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 3144 Number of extensions: 152 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 1197 Length of database: 1139 Length adjustment: 47 Effective length of query: 1150 Effective length of database: 1092 Effective search space: 1255800 Effective search space used: 1255800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory