GapMind for catabolism of small carbon sources

 

Alignments 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)



>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.

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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:

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