Alignments for a candidate for ofo in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Pseudomonas stutzeri RCH2

Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate GFF3452 Psest_3517 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>FitnessBrowser__psRCH2:GFF3452
          Length = 1156

 Score = 2316 bits (6001), Expect = 0.0
 Identities = 1156/1156 (100%), Positives = 1156/1156 (100%)

Query: 1    MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60
            MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL
Sbjct: 1    MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60

Query: 61   DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120
            DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD
Sbjct: 61   DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120

Query: 121  RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180
            RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL
Sbjct: 121  RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180

Query: 181  DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240
            DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD
Sbjct: 181  DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
            PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD
Sbjct: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300

Query: 301  EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360
            EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK
Sbjct: 301  EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360

Query: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420
            RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA
Sbjct: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420

Query: 421  RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWI 480
            RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWI
Sbjct: 421  RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWI 480

Query: 481  GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL 540
            GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL
Sbjct: 481  GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL 540

Query: 541  RVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSV 600
            RVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSV
Sbjct: 541  RVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSV 600

Query: 601  IIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKR 660
            IIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKR
Sbjct: 601  IIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKR 660

Query: 661  EIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVLI 720
            EIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVLI
Sbjct: 661  EIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVLI 720

Query: 721  PGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIA 780
            PGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIA
Sbjct: 721  PGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIA 780

Query: 781  AGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAI 840
            AGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAI
Sbjct: 781  AGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAI 840

Query: 841  SDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSA 900
            SDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSA
Sbjct: 841  SDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSA 900

Query: 901  KLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRY 960
            KLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRY
Sbjct: 901  KLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRY 960

Query: 961  RQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYK 1020
            RQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYK
Sbjct: 961  RQLVERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYK 1020

Query: 1021 LQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVER 1080
            LQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVER
Sbjct: 1021 LQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVER 1080

Query: 1081 QLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQL 1140
            QLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQL
Sbjct: 1081 QLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQL 1140

Query: 1141 AKGDEVQSVRLFQPAA 1156
            AKGDEVQSVRLFQPAA
Sbjct: 1141 AKGDEVQSVRLFQPAA 1156


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: 3698
Number of extensions: 124
Number of successful extensions: 1
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: 1156
Length of database: 1156
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1109
Effective search space:  1229881
Effective search space used:  1229881
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 (21.8 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

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