Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate H281DRAFT_05847 H281DRAFT_05847 indolepyruvate ferredoxin oxidoreductase
Query= reanno::Marino:GFF880 (1172 letters) >FitnessBrowser__Burk376:H281DRAFT_05847 Length = 1199 Score = 1126 bits (2912), Expect = 0.0 Identities = 569/1177 (48%), Positives = 793/1177 (67%), Gaps = 44/1177 (3%) Query: 8 LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQ 67 L L+D+Y E GR +++G QALVR+P++Q DR GLNTAG +SGYRGSPLG +DQ Sbjct: 17 LSSVTLDDKYTLERGRAYMSGIQALVRLPMLQQERDRAAGLNTAGFISGYRGSPLGGLDQ 76 Query: 68 ALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRA 127 +LW+AK L +++ F P +NEDLAAT + G+QQV + +GVF +WYGKGPGVDR+ Sbjct: 77 SLWKAKQHLASHQVVFQPGVNEDLAATAVWGSQQVNLYPSAKYDGVFSMWYGKGPGVDRS 136 Query: 128 GDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEF 187 GD KHG + GSS HGGVLV+AGDDH SS++ HQS+ F + +P + P+N+ EYL+F Sbjct: 137 GDVFKHGNSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLFPSNVQEYLDF 196 Query: 188 GLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDLP 246 GL G+A+SRYSG WV K +++ VES+ASV+I P + P+DF PE GL+ RWPD P Sbjct: 197 GLHGWAMSRYSGLWVAMKCVTDVVESSASVDIDPHRTQIILPEDFAMPEGGLNIRWPDPP 256 Query: 247 GPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306 Q +++K A A+ RAN++DR D+ ARFGI+T GK +LD+ +AL LG+D++ Sbjct: 257 LVQEARLLDYKWYAALAYVRANKLDRVEIDSPHARFGIMTGGKAYLDVRQALTDLGLDDE 316 Query: 307 KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEV 366 +G+ +YKVG VWPLE +G F G +E+LV+EEKR I+E IKE + Sbjct: 317 TCSRIGIRLYKVGCVWPLEAQGAQAFARGLDEILVVEEKRQILEYAIKEELYNWPDAQRP 376 Query: 367 LITGKQDE-----------LGRPLIPYVGELSPKLVAGFLAARLGRF-FEVDFSERMAEI 414 + GK DE +G L+P ELSP ++A +A RL +F D R+A Sbjct: 377 RVFGKFDEKDGAGGEWSVPMGNWLLPAHYELSPAIIAKAIATRLDKFDLPSDVRARIAAR 436 Query: 415 SAMTTAQDPG------GVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTE 468 A+ A++ V+R P+FCSGCPHNTST VPEGS+A+AGIGCH+M WM R+T Sbjct: 437 IAVIEAKEKALARPRVEVERKPWFCSGCPHNTSTNVPEGSRAMAGIGCHYMTVWMDRSTS 496 Query: 469 SLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDA 528 + QMGGEGV WIG++ +T + HVF NLG+GTYFHSG +AIR A+A+ NITYK+L+NDA Sbjct: 497 TFSQMGGEGVAWIGQAPFTNDKHVFANLGDGTYFHSGLLAIRAAIASKANITYKLLYNDA 556 Query: 529 VAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELD 588 VAMTGGQPVDG +TV +I Q+AAEG ++ +++DEPEKY G+ L P + H R +LD Sbjct: 557 VAMTGGQPVDGVLTVPQITHQLAAEGATKIAIVTDEPEKYSGNVGLAP-GIDIHHRDQLD 615 Query: 589 QVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNC 648 +VQR+LR+IPG T+LIYDQTCA EKRRRRKR +PDPA+R IN VCEGCGDCSV+SNC Sbjct: 616 EVQRQLREIPGTTILIYDQTCATEKRRRRKRGAYPDPARRVVINEAVCEGCGDCSVKSNC 675 Query: 649 LSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLA 708 LSV P TE G KR+I+QS+CNKDFSCVNGFCPSFV++EGGQLRK + ++ + Sbjct: 676 LSVEPLDTEYGTKRQINQSTCNKDFSCVNGFCPSFVSVEGGQLRKPKA--ASGIVADAMP 733 Query: 709 DIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVL 768 +P P LP + Y +LV GVGGTGVVT+G L+ MAAHLE++G +VLD G AQKGG V+ Sbjct: 734 PVPEPTLPSIARPYGVLVTGVGGTGVVTIGALLGMAAHLENKGVTVLDVTGLAQKGGAVM 793 Query: 769 SYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTAD 828 S+V++A +P +H RI+ G+A VI CD +V +S + +S ++ TR+V N A PTA+ Sbjct: 794 SHVQIANNPGDIHATRIAMGEASLVIGCDAIVTASDECVSRMQAGRTRVVLNSAHTPTAE 853 Query: 829 YV-----LFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAW 883 + F + +AD R G G++ D +DAN A L+GD +++N +LG+AW Sbjct: 854 LIKNPNWRFPGSSTEADVRAG-----AGDECVDTVDANHFAVALLGDAIYTNPFVLGYAW 908 Query: 884 QKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAV---------TDLLDDSN 934 Q+G +PL+ +LM+AIELN V +++N+ AF WGR +A DP A+ D + Sbjct: 909 QRGWVPLTYQSLMRAIELNNVQVEKNRAAFEWGRRAAHDPVALRKYAQSQGQAGASDTPS 968 Query: 935 AQVVEVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLG--ETNLLLTR 992 +++ + LD LI+ R +L +QN +AD+YR V+ VR AE +L + L LT Sbjct: 969 GKIISLHTPKALDTLIDKRATYLAAWQNDAYADRYRALVSQVRVAESALDSIDGQLPLTE 1028 Query: 993 AVAQQLYRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRP 1052 VA+ L++ MAYKDEYEVARL+++ F++++ +FEGD+K+H HLAPP+ S + DA G Sbjct: 1029 TVAKNLHKLMAYKDEYEVARLYSDPAFIEKLKASFEGDWKLHIHLAPPMFS-KKDAHGHL 1087 Query: 1053 KKRRFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNAS 1112 K+++GPW+F A +LAK + LRGTA+D F + +R+ +RA++ +Y++LV + L Sbjct: 1088 IKKKYGPWVFSAMHVLAKFKFLRGTALDVFGKTEERRTERALIGEYEALVRELIGGLTVQ 1147 Query: 1113 NYETFLQLAELPADVRGYGPVREQAAESIREKQTQLI 1149 N + ++LA LP +RG+G ++E + +R K +L+ Sbjct: 1148 NRDLAVELANLPDGIRGFGHIKENNLKGVRVKWNELL 1184 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: 3194 Number of extensions: 149 Number of successful extensions: 10 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: 1199 Length adjustment: 47 Effective length of query: 1125 Effective length of database: 1152 Effective search space: 1296000 Effective search space used: 1296000 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