GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iorAB in Paraburkholderia bryophila 376MFSha3.1

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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05847 H281DRAFT_05847
            indolepyruvate ferredoxin oxidoreductase
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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