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

GapMind for catabolism of small carbon sources

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

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_3961
          Length = 512

 Score =  674 bits (1739), Expect = 0.0
 Identities = 341/481 (70%), Positives = 391/481 (81%), Gaps = 8/481 (1%)

Query: 3   LHQNLIAGEWVGGDGVA---NINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSG 59
           +H NLI G W   DGV    N NPS+T DV+G+YA AS E A  A+AAA AAFPAWS S 
Sbjct: 34  MHANLIGGAWT--DGVRTYQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLST 91

Query: 60  ILERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAG 119
             +R  IL    +EI+ARK ELG LL+REEGKTL E IGE  RA  IF+FFAGE LR  G
Sbjct: 92  PQQRFDILDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALRPGG 151

Query: 120 EVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGC 179
           EV+PSVRPG+G+EITREP G +GIITPWNFPIAIPAWK+APAL YGN +VFKPAE+VPG 
Sbjct: 152 EVMPSVRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGS 211

Query: 180 SWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEH 239
           +WA+ DILHRAGLP GV NLVMG+GS VG  +L+   +  ++FTGS  TG+RVA A V  
Sbjct: 212 AWALADILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRVAAACVPR 271

Query: 240 NRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAA 299
             K QLEMGGKNPFVVLDDADL+VAV AA+NS FFSTGQRCTASSR+IVTEGIHDRFVAA
Sbjct: 272 GAKVQLEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFVAA 331

Query: 300 MGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRD---T 356
           M E++K L VDDA K GT IGPVVD  QL QD +YI IG+QEGAKLA+GGE + ++    
Sbjct: 332 MVEKMKTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADGA 391

Query: 357 PGFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSL 416
           PGFYL+PALFTE T  MRI+REEIFGPV +V+R K+Y+EALA+ANDTPFGL+SGIATTSL
Sbjct: 392 PGFYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATTSL 451

Query: 417 KHATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTL 476
           KHATHFKR+A+AGMVMVNLPTAGVD+HVPFGGRK+SSYGPREQG+YAAEFYT VKTAYT 
Sbjct: 452 KHATHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKSSSYGPREQGRYAAEFYTTVKTAYTQ 511

Query: 477 A 477
           A
Sbjct: 512 A 512


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: 815
Number of extensions: 32
Number of successful extensions: 3
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: 512
Length adjustment: 34
Effective length of query: 443
Effective length of database: 478
Effective search space:   211754
Effective search space used:   211754
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: 52 (24.6 bits)

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

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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, 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

GapMind for catabolism of small carbon sources