Alignments for a candidate for dopDH in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Sinorhizobium fredii NGR234

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_012708927.1 NGR_RS23205 aldehyde dehydrogenase family protein

Query= reanno::Smeli:SM_b20891
         (477 letters)



>NCBI__GCF_000018545.1:WP_012708927.1
          Length = 477

 Score =  892 bits (2304), Expect = 0.0
 Identities = 444/477 (93%), Positives = 464/477 (97%)

Query: 1   MTLHQNLIAGEWVGGDGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGI 60
           MTLHQNLIAGEWVGGDG+AN+NPSNT+DVVGEYARASAEDA AAIAAAKAAFPAWSRSGI
Sbjct: 1   MTLHQNLIAGEWVGGDGIANVNPSNTNDVVGEYARASAEDASAAIAAAKAAFPAWSRSGI 60

Query: 61  LERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGE 120
           LERHAIL+KTADEILARKDELGRLLSREEGKTLAEGIGET+RA QIF+FFAGE LRLAGE
Sbjct: 61  LERHAILRKTADEILARKDELGRLLSREEGKTLAEGIGETIRASQIFDFFAGECLRLAGE 120

Query: 121 VVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCS 180
            +PSVRP IGVEI+REP GVVGIITPWNFPIAIPAWK+APAL YGNT+VFKPAELVPGCS
Sbjct: 121 TLPSVRPNIGVEISREPVGVVGIITPWNFPIAIPAWKIAPALAYGNTVVFKPAELVPGCS 180

Query: 181 WAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHN 240
           WAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGST TGKRVA+ASVEHN
Sbjct: 181 WAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTGTGKRVALASVEHN 240

Query: 241 RKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAM 300
           RK+QLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSR+IVTEGIHD+FVAAM
Sbjct: 241 RKFQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRVIVTEGIHDKFVAAM 300

Query: 301 GERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFY 360
           GER+KGLVVDDALK GTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGE+ISRDTPGFY
Sbjct: 301 GERMKGLVVDDALKAGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGELISRDTPGFY 360

Query: 361 LQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHAT 420
           LQPALFTEATN MRISREEIFGPVAAVIRVKDY+EAL VANDTPFGLS+GIATTSLKHAT
Sbjct: 361 LQPALFTEATNAMRISREEIFGPVAAVIRVKDYEEALNVANDTPFGLSAGIATTSLKHAT 420

Query: 421 HFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTLA 477
           HFKRN+EAGMVMVNLPTAGVDFHVPFGGRK SS+GPREQGKYAAEFYT VKTAYTLA
Sbjct: 421 HFKRNSEAGMVMVNLPTAGVDFHVPFGGRKGSSHGPREQGKYAAEFYTTVKTAYTLA 477


Lambda     K      H
   0.317    0.134    0.391 

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: 877
Number of extensions: 16
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: 477
Length of database: 477
Length adjustment: 33
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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