Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate Dsui_0379 Dsui_0379 indolepyruvate ferredoxin oxidreductase, alpha/beta subunit
Query= reanno::Marino:GFF880 (1172 letters) >FitnessBrowser__PS:Dsui_0379 Length = 1183 Score = 1128 bits (2918), Expect = 0.0 Identities = 587/1174 (50%), Positives = 788/1174 (67%), Gaps = 32/1174 (2%) Query: 7 QLDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVD 66 +L L+D+Y SGR FLTGTQAL+R+P++Q D+ QGLNTAG +SGYRGSPLG +D Sbjct: 11 ELASASLDDKYTTLSGRAFLTGTQALIRLPMLQRLRDQAQGLNTAGFISGYRGSPLGGLD 70 Query: 67 QALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDR 126 Q LW+A+ L EN I F P +NEDLAAT + G+QQV + +GVF LWYGKGPGVDR Sbjct: 71 QGLWKAQKYLAENHITFQPGVNEDLAATAVWGSQQVNLFPGAKYDGVFALWYGKGPGVDR 130 Query: 127 AGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLE 186 +GD +H GSS HGGVLVVAGDDH SS++PHQ++ F + MP + PAN+ EYLE Sbjct: 131 SGDVFRHANAAGSSRHGGVLVVAGDDHAAKSSTLPHQTEHVFKAVMMPVLYPANVQEYLE 190 Query: 187 FGLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDL 245 +GL G+A+SRYSGCWV FKA+++TVE++ASV + P A D PDDF P GL+ RWPD Sbjct: 191 YGLHGWAMSRYSGCWVAFKALADTVETSASVWVDPMALDIRLPDDFELPADGLNIRWPDP 250 Query: 246 PGPQLETRIEH-KLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGID 304 P Q E R+ H KL A A+ARANR++R + D+ R GI+T GK +LD+++ALD LGID Sbjct: 251 PLVQ-EARLTHFKLYAALAYARANRLNRIVIDSPAPRLGIITAGKSYLDVMQALDELGID 309 Query: 305 EDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPG 364 + A +G+ +YKVGMVWPLE G+ F G +E+LV+EEKR ++E Q+KE + Sbjct: 310 QQLAAQIGIRLYKVGMVWPLESEGVRQFAEGLDEILVVEEKRQMLEYQLKEELYNWREDV 369 Query: 365 EVLITGKQDELGR---------------PLIPYVGELSPKLVAGFLAARLGRFF-EVDFS 408 + GK DE G L+P GELS +A +A+R+ R F Sbjct: 370 RPRVVGKFDEKGEWALLPDGKGHLAHGDWLLPAAGELSVAQIARAIASRIERHFTSPAIK 429 Query: 409 ERMAEISAMTTAQDPGGV--KRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRN 466 R+ I A A + +R P+FCSGCPHNTST+VPEGS+A+AGIGCH+M +WM R+ Sbjct: 430 ARLDLIEAKQKALQTPLILTQRTPHFCSGCPHNTSTRVPEGSRAVAGIGCHYMVTWMDRS 489 Query: 467 TESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFN 526 T + MGGEGV W+G++ +T H+F NLG+GTYFHSG +AIRQ+VAA NITYKIL+N Sbjct: 490 TSTFTHMGGEGVTWVGQAPFTEEKHIFANLGDGTYFHSGLLAIRQSVAAKTNITYKILYN 549 Query: 527 DAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSE 586 DAVAMTGGQPVDG ++V RI +Q+ AEGV R+V+++DEPEKY DL P +V R E Sbjct: 550 DAVAMTGGQPVDGILSVPRITRQLEAEGVGRMVIVTDEPEKYAEVTDLAP-NVPVRHRDE 608 Query: 587 LDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQS 646 LD VQRELR+IPG T+LIYDQTCA EKRRRRKR + D +R FIN VCEGCGDCSVQS Sbjct: 609 LDAVQRELREIPGTTILIYDQTCATEKRRRRKRGKLADVDRRVFINEAVCEGCGDCSVQS 668 Query: 647 NCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRK 706 NCLSV+P +T+ GRKR IDQS+CNKDFSC+ GFCPSFVT+EG +L+K + + ++ + Sbjct: 669 NCLSVIPVETDFGRKRAIDQSNCNKDFSCLKGFCPSFVTLEGAKLKKGQAL---AMDAQD 725 Query: 707 LADIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGT 766 +P P LP Y+LLV GVGGTGVVT+G LI MAAHL+ +G SVLD G AQK G Sbjct: 726 WPPLPEPVLPPTARPYNLLVTGVGGTGVVTLGALIGMAAHLDGKGVSVLDMTGLAQKYGA 785 Query: 767 VLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPT 826 V +++R A P+ +H RI+ G+ADA++ D+VV + +ALS + TR V N E PT Sbjct: 786 VFTHLRFADRPEDIHAARIATGEADAILGGDVVVTAGNEALSKMLEGRTRAVVNCTETPT 845 Query: 827 ADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKG 886 A++ D + + VG DH LDA +A LMGD +++N+ +LG+AWQKG Sbjct: 846 AEFTRNPDWQFPLARMQQTVTATVGADHAWFLDAQALATALMGDALYTNMFLLGYAWQKG 905 Query: 887 LLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTL 946 L+P+S AL +AIELNG A+ N +A WGR +AVD + V L + A +P+ L Sbjct: 906 LVPVSLPALGRAIELNGTAVAANLQALDWGRRAAVDEARVRQLATPA-ADTPPPRPDAAL 964 Query: 947 DELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKD 1006 +E++ R + L +YQ+ A +YR + +R+AE L + L +T A A+ ++ +A KD Sbjct: 965 EEVLALREQELTDYQDAALARRYRQRIEALRQAEAPL-DPALPVTLAAARNYFKVLAIKD 1023 Query: 1007 EYEVARLFAETDFMKEVNETFEG----DFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMF 1062 EYEVARL +F + +TF G D+ VH HLAPPL + G+ +KR++GPWM Sbjct: 1024 EYEVARLHTRPEFFARLRQTFAGEPGKDYAVHVHLAPPLWARPDPRSGQIRKRQYGPWML 1083 Query: 1063 RAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNA-SNYETFLQLA 1121 A +LLA+L+ LRGTA+D F ++A+R+++RA+ Y++ ++RI L A S + L+LA Sbjct: 1084 GALKLLARLKFLRGTALDVFGHTAERRMERALQAGYEADLERILEALAAGSAHPALLELA 1143 Query: 1122 ELPADVRGYGPVREQAAESIREKQTQLIKALDTG 1155 LP VRGYG V+ +AE R+++ +L++ L+ G Sbjct: 1144 RLPESVRGYGHVKAASAEKARQQRQELLRKLEGG 1177 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: 3147 Number of extensions: 130 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: 1183 Length adjustment: 47 Effective length of query: 1125 Effective length of database: 1136 Effective search space: 1278000 Effective search space used: 1278000 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