Alignments for a candidate for iorAB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Acidovorax sp. GW101-3H11

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate Ac3H11_2707 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

Query= reanno::Marino:GFF880
         (1172 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2707
          Length = 1161

 Score = 1123 bits (2905), Expect = 0.0
 Identities = 583/1159 (50%), Positives = 784/1159 (67%), Gaps = 38/1159 (3%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            L D+Y   +GRV++ GTQALVR+ L Q A D   GLNT G VSGYRGSPLGAVDQ LW+ 
Sbjct: 7    LADKYELPAGRVYMNGTQALVRLLLAQKARDEAAGLNTEGFVSGYRGSPLGAVDQELWKN 66

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            + LLD++++ F P +NE+LAAT + GTQ V  D   +V+GVF LWYGKGPGVDR+GD  K
Sbjct: 67   RALLDKHKVRFQPGLNEELAATSVWGTQMVSLDPKARVDGVFALWYGKGPGVDRSGDVFK 126

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            HG   G +PHGGVL+VAGDDH C SSS+PHQS+ AF++  +P ++P+ + E++EFGL GY
Sbjct: 127  HGNIAGGAPHGGVLLVAGDDHACKSSSLPHQSEHAFIAAMIPVLHPSGVNEFIEFGLHGY 186

Query: 193  ALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDLPGPQLE 251
            A+SRYSGCWVGFK IS+TVES++S +I P + +   P  +  P  G   RWPD P  Q  
Sbjct: 187  AMSRYSGCWVGFKVISDTVESSSSFDIDPMSVEIKIPQSYPVPADGFSIRWPDPPLEQEN 246

Query: 252  TRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDEDKARDM 311
                 +L A+  + R N+++R  +   +AR GI TTGK +LD+ EAL LLG+DE  A+ +
Sbjct: 247  RLQRERLYALLEYVRLNKLNRQDWAVPDARLGICTTGKSYLDVREALSLLGLDEAAAQAL 306

Query: 312  GLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYM-SEPDRPGEVLITG 370
            G+ + K+G+VWPLE   +++F  G +E+LV+EEKR ++E QIKE++ +EP RP    + G
Sbjct: 307  GVRLLKIGVVWPLEPTCVVEFAQGLDEILVVEEKRQVLEYQIKEHLYNEPHRP---RVVG 363

Query: 371  KQDELGR--------PLIPYVGELSPKLVAGFLAARLGRFFEVD--------FSERMAEI 414
            K DE G          L+   GEL+P  +A  +AARL + +           + ER A +
Sbjct: 364  KYDESGEWVQVPSSGILLSPNGELTPAGIADVIAARLVKVYGQGVLPESVRVWLERQAVV 423

Query: 415  SAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMG 474
            +  + +  P   +R+PYFCSGCPHNTST+VPEGS+ALAGIGCH+M+ WM R TE+  QMG
Sbjct: 424  ATRSPSDAP-VPQRLPYFCSGCPHNTSTQVPEGSRALAGIGCHYMSMWMDRRTETFSQMG 482

Query: 475  GEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGG 534
            GEGV WIG++ YT  PHVF NLG+GTY HSGS+AIR AVAAG+NITYK+L NDAVAMTGG
Sbjct: 483  GEGVPWIGQAPYTDTPHVFANLGDGTYMHSGSLAIRAAVAAGVNITYKLLVNDAVAMTGG 542

Query: 535  QPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQREL 594
            QPV+G  +V ++ +Q+AAEGV  + ++SDEPE +    D FPKDV    R  +D +QR L
Sbjct: 543  QPVEGAPSVPQLLRQLAAEGVKELHLVSDEPEAFQALDD-FPKDVKVSHRDGMDALQRAL 601

Query: 595  RDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPR 654
            RD+ G +V++Y QTCAAEKRRRRK+K   DPA+R  IN  VCEGCGDC VQSNC+S++P 
Sbjct: 602  RDVKGVSVIVYAQTCAAEKRRRRKKKTLADPARRVVINEAVCEGCGDCGVQSNCVSILPL 661

Query: 655  KTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPK 714
            +T LGRKR+IDQS CNKDFSCV GFCPSFV ++G +LRK +              +  P+
Sbjct: 662  ETPLGRKRQIDQSGCNKDFSCVRGFCPSFVVLDGAELRKPQRDRVAPP-----TGMARPE 716

Query: 715  LPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMA 774
            LP +   +++LV GVGGTGVVT+G L+ MAAHLE +G  VLD  G AQKGG V+S+VR+A
Sbjct: 717  LPVLARPWNILVAGVGGTGVVTIGALMGMAAHLEGKGVLVLDMAGLAQKGGAVMSHVRLA 776

Query: 775  PSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRD 834
              P +LH  R++ GQAD V+ CDL+VA++  AL+ +    TR V N    PT  +   RD
Sbjct: 777  ADPVQLHAARVARGQADVVLGCDLMVAAAGDALASMASGRTRAVLNTDVAPTGSFT--RD 834

Query: 835  ADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAA 894
             D +A     L +        + L+A+ +A  LMGD V +NV +LGFAWQKG +PL E +
Sbjct: 835  PDWQASPDAMLERVGSAAAQVESLEASRLAVALMGDAVATNVFLLGFAWQKGWVPLQEDS 894

Query: 895  LMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPT--LDELINT 952
            L++AIELNG A+  N+ AF WGR +A+DP+AV       + + V + P  T  L  ++  
Sbjct: 895  LLRAIELNGAAVGMNRAAFAWGRQAALDPAAVRRAAGLPSDEKVMLMPSRTASLASILAD 954

Query: 953  RHKHLVNYQNQRWADQYRDAVAGVRKAEESL--GETNLLLTRAVAQQLYRFMAYKDEYEV 1010
            R + L +YQN R+A  Y   V  V   E++   GE    L R VA  LY+ MAYKDEYEV
Sbjct: 955  RTERLADYQNARYAQHYAAVVRRVSDVEKARVGGER---LAREVAMSLYKLMAYKDEYEV 1011

Query: 1011 ARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAK 1070
            ARL   +DF+  + E FEGDF V ++LAPPLL+   DAQGRP K+R+G W+  AFRLLA+
Sbjct: 1012 ARLHTSSDFLARLQERFEGDFTVSYYLAPPLLA-RRDAQGRPVKQRYGAWVQTAFRLLAR 1070

Query: 1071 LRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGY 1130
            LR LRGT  DPF ++ +R+ +RA + ++++LV+ + ++LN++N+   L LA LP  VRGY
Sbjct: 1071 LRFLRGTVFDPFGWTRERREERAAIDEFEALVEDLLKDLNSNNFNEALALARLPQQVRGY 1130

Query: 1131 GPVREQAAESIREKQTQLI 1149
            G V+ +  E  ++K  +L+
Sbjct: 1131 GHVKAREHEVAQKKALELL 1149


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: 3055
Number of extensions: 125
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: 1161
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1114
Effective search space:  1253250
Effective search space used:  1253250
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources