Alignments for a candidate for adh in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Pseudovibrio axinellae Ad2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_068009265.1 PsAD2_RS18325 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_001623255.1:WP_068009265.1
          Length = 498

 Score =  530 bits (1365), Expect = e-155
 Identities = 263/486 (54%), Positives = 347/486 (71%), Gaps = 10/486 (2%)

Query: 45  DLLRGDSFVGGRWLPTP-------ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAF 97
           DLL   +FVGG W+ +        A F V +P++   + ++ + G  E + A+  AY A 
Sbjct: 16  DLLINAAFVGGEWISSNDFASNNGALFDVVNPSTDDLIASLPNMGRAETKTAIDLAYVAQ 75

Query: 98  SSWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSE 157
             W + + KER+++LRKW++LM+ N D+LA I+TAE GKP++EA+GEI+Y A F+EWF E
Sbjct: 76  KEWAKRTGKERAAVLRKWFELMVANADDLAVILTAEMGKPVQEAKGEIMYGASFVEWFGE 135

Query: 158 EARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKP 217
           EA+RVYGDII     DKR +VLKQP+GV   ITPWNFP+AMI RK+  ALA GC  V KP
Sbjct: 136 EAKRVYGDIIPGHQSDKRIMVLKQPIGVVGSITPWNFPNAMIARKIAPALAVGCAFVAKP 195

Query: 218 AEDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATG 277
           A++TP SALA+A LA +AG+P G+++VI  + T + ++G+  C +  V K++FTGST  G
Sbjct: 196 ADETPLSALAMALLAEEAGLPKGLFSVI--TSTLSSDIGKEFCENEKVRKLTFTGSTQVG 253

Query: 278 KILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQ 337
           +IL+  +A+ V + SMELGG AP IVFD A++D AV GAM SKFRN GQTCVCSNR  VQ
Sbjct: 254 RILMRQSADQVMKTSMELGGNAPLIVFDDADLDAAVEGAMISKFRNNGQTCVCSNRIYVQ 313

Query: 338 RGIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTG 397
             +++ F  K   A+KK ++VG+GFEE    GPLI+E AV+KVE+H+ DA  KGA +VTG
Sbjct: 314 AAVYEDFTQKLVAAVKK-MKVGDGFEENVVAGPLISEAAVKKVEEHIKDASDKGAEIVTG 372

Query: 398 GKRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGY 457
           G RHQ GG FFEPT+L+ V + M    EETFGPVAP+ KFD  ++ +  AN    GLA Y
Sbjct: 373 GARHQLGGTFFEPTVLTGVKQGMRIAKEETFGPVAPLFKFDSVDDVIEQANDTIFGLASY 432

Query: 458 FYSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKY 517
           FY+ D +++W+VAE LE GMVGVN GLIS+   PFGG+KQSG GREGSKYG D+YLE+KY
Sbjct: 433 FYANDLSRVWQVAEALEYGMVGVNTGLISTEVAPFGGIKQSGSGREGSKYGCDDYLEIKY 492

Query: 518 VCYGGL 523
           VC GG+
Sbjct: 493 VCVGGV 498


Lambda     K      H
   0.318    0.135    0.400 

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: 635
Number of extensions: 20
Number of successful extensions: 4
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: 523
Length of database: 498
Length adjustment: 34
Effective length of query: 489
Effective length of database: 464
Effective search space:   226896
Effective search space used:   226896
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 24 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)
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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