Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate H281DRAFT_01671 H281DRAFT_01671 indolepyruvate ferredoxin oxidoreductase
Query= reanno::Marino:GFF880 (1172 letters) >FitnessBrowser__Burk376:H281DRAFT_01671 Length = 1184 Score = 1063 bits (2749), Expect = 0.0 Identities = 555/1171 (47%), Positives = 768/1171 (65%), Gaps = 22/1171 (1%) Query: 1 MSADTPQLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGS 60 + +T + L+D+Y +E G +++G+ AL+R+ + Q D GLNTAG VSGYRGS Sbjct: 6 IEVETAPTSEVSLDDKYRKERGYAYMSGSHALIRVMINQRIRDNDAGLNTAGFVSGYRGS 65 Query: 61 PLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVET-DEDRQVEGVFGLWYG 119 PL D ALW A+ +L +++I F+PAINEDLAAT + GTQQ+ ++ VEGVF +WYG Sbjct: 66 PLAGFDTALWSAEAVLKQHQIKFLPAINEDLAATAVWGTQQLALFPQESTVEGVFSMWYG 125 Query: 120 KGPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPA 179 KGPGVDR+GDALKHG G+S GGVLV A DDH SS+ HQS+ A ++ F+P + PA Sbjct: 126 KGPGVDRSGDALKHGNGAGTSALGGVLVAAADDHTAKSSTFGHQSEQALIAAFIPVLYPA 185 Query: 180 NIAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPPAP-DFVTPDDFTAPESGL 238 ++ +YL+FG+ G A+ RYSG W+G K +S+ +E++A ++ P D PD A + L Sbjct: 186 SVQDYLDFGVLGIAMGRYSGLWIGLKCVSDVIETSAVADVDPHRIDIRLPDKEFAADDDL 245 Query: 239 HYRWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEAL 298 H R PD+ Q + +L A AF RANR++ +++ GI+ GK + D++EAL Sbjct: 246 HIRSPDVWAEQEPRIVRKRLPAALAFCRANRLNSIRIKGPKSKLGIMCAGKAYNDVMEAL 305 Query: 299 DLLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMS 358 LLG+ +D GL + K+GMVWPL+ + DF G +E+LV+EEKR IIE QIK+ + Sbjct: 306 RLLGLSDDDIEKNGLAVLKIGMVWPLDPTILRDFAAGLDELLVVEEKRPIIEQQIKDELY 365 Query: 359 EPDRPGEVLIT----------GKQDELGRP-LIPYVGELSPKLVAGFLAARLG------R 401 G L+ G+ + G L+ EL+P VAG + ARL Sbjct: 366 SDALNGLPLVRVSGKGSGAIGGEWNRSGEACLLRSDYELTPVEVAGAIVARLRAQAGWTE 425 Query: 402 FFEVDFSERMAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMAS 461 + + R+A + A+ Q G R P+FCSGCPHNTST+VPEGS+A AGIGCH+MAS Sbjct: 426 TRKREIEARLAALEAVGRVQAVAGAIRKPFFCSGCPHNTSTRVPEGSRATAGIGCHYMAS 485 Query: 462 WMGRNTESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITY 521 M R TES MGGEGV W+ +++++ H+F N+G+GTYFHSGS+AIRQAVAA +++T+ Sbjct: 486 SMDRRTESYTHMGGEGVPWVAQAQFSTRKHIFANIGDGTYFHSGSLAIRQAVAARVSMTF 545 Query: 522 KILFNDAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTF 581 KIL+NDA AMTGGQPVDG++TVD I +Q+AAEGV R+ V+SD+ E+Y F T Sbjct: 546 KILYNDAAAMTGGQPVDGELTVDGITRQVAAEGVRRIAVVSDDIEQYRISGTTFAAGTTV 605 Query: 582 HDRSELDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGD 641 HDRSELD VQR LRD G +VL+YDQTCA+EKRRRRK+ +PDPAKR IN VCEGCGD Sbjct: 606 HDRSELDAVQRNLRDYEGVSVLVYDQTCASEKRRRRKKGTYPDPAKRVAINSEVCEGCGD 665 Query: 642 CSVQSNCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGS 701 CSVQSNCLSV P T LGRKR+I+QSSCNKDFSCV GFCPSFV++EGG+LR S+ + Sbjct: 666 CSVQSNCLSVEPLDTPLGRKRQINQSSCNKDFSCVQGFCPSFVSVEGGKLRSSQTKKSPE 725 Query: 702 VLTRKLADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFA 761 + ++P P P MT + D+L+ GVGGTGVVT+G L+ MAAHLE RG +VLD G A Sbjct: 726 AMMADWPELPYPASPAMTDTVDILINGVGGTGVVTIGNLLGMAAHLEGRGCTVLDMAGLA 785 Query: 762 QKGGTVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANE 821 QKGG V S+VR+A ++++ RI +G AD +I CDLVV ++ LS +R TR+V N Sbjct: 786 QKGGAVWSHVRLASKRERMYASRIPSGSADVIIGCDLVVTAAPDTLSRIRKGKTRVVING 845 Query: 822 AELPTADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGF 881 PT+ +V RD + + +++ G+D D +DA IA + +GDTVFSN +MLGF Sbjct: 846 QTSPTSAFVANRDWQLPEAELKSHVESVCGDDFVDWVDAQEIARRHLGDTVFSNAIMLGF 905 Query: 882 AWQKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVK 941 WQ+GL+PL+ ++ +AIELNG A+ +NK AF GR AV+P+ + + V K Sbjct: 906 VWQQGLIPLARESIERAIELNGQAVKKNKLAFQIGRWLAVNPARFAAGEEVESVIVWRQK 965 Query: 942 PEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRF 1001 + LDELI +R L YQ++R+A +Y V+ + S G+ + AVA+ LY+ Sbjct: 966 KKVVLDELIQSRVSLLAAYQSERYAREYETFVSEITAQVGSHGKREAFIL-AVAEGLYKL 1024 Query: 1002 MAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWM 1061 MAYKDEYEVARL++ F K + FEGDFK+ ++LAPP+LS + + +G K+ FGPW+ Sbjct: 1025 MAYKDEYEVARLYSLPGFKKSLENQFEGDFKIRYYLAPPMLSRKNE-KGELIKKEFGPWL 1083 Query: 1062 FRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLA 1121 F LLA+L+ LRGT DPF ++A+R+ +RA++++Y+ + R A + ++LA Sbjct: 1084 GHVFPLLARLKILRGTPFDPFGHTAERRRERALIREYRLWI-RTALTHLADKPDVCIELA 1142 Query: 1122 ELPADVRGYGPVREQAAESIREKQTQLIKAL 1152 +LP +RGYG V+E+A + + K+ L+ AL Sbjct: 1143 KLPDSIRGYGHVKERAIDEVMAKRDTLLAAL 1173 Lambda K H 0.319 0.136 0.405 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: 2962 Number of extensions: 110 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: 1172 Length of database: 1184 Length adjustment: 47 Effective length of query: 1125 Effective length of database: 1137 Effective search space: 1279125 Effective search space used: 1279125 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