Aligments for a candidate for adh in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Acidovorax sp. GW101-3H11

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate Ac3H11_4393 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::psRCH2:GFF2231
         (506 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4393
          Length = 507

 Score =  763 bits (1969), Expect = 0.0
 Identities = 365/505 (72%), Positives = 426/505 (84%)

Query: 2   IYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKA 61
           +YA PG PGA +++KP+Y N+IGG+FVPPVKG+YF   +PV+G+V     RS AEDIE A
Sbjct: 3   VYAAPGAPGAKITYKPQYDNFIGGKFVPPVKGQYFDVITPVSGKVYTRAARSTAEDIELA 62

Query: 62  LDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLA 121
           LDAAHAAAD+WGKT    RA ILLKIA+RIE NLE+LA AET DNGKA+RETLNAD+PL 
Sbjct: 63  LDAAHAAADSWGKTDAATRANILLKIANRIEENLERLAYAETVDNGKAIRETLNADIPLT 122

Query: 122 ADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAA 181
            DHFRYFAGC+RAQEG+ + I+E+T AYH  EPLGVVGQIIPWNFP+LMAAWKLAPAL A
Sbjct: 123 VDHFRYFAGCVRAQEGALSNIDENTVAYHIQEPLGVVGQIIPWNFPILMAAWKLAPALGA 182

Query: 182 GNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTGS 241
           GNC+VLKPAE TP+SI++ +E++ DLLPPGVLNIV GFGREAG  LA S RIAKIAFTGS
Sbjct: 183 GNCVVLKPAESTPISILILVELIADLLPPGVLNIVNGFGREAGMPLAQSKRIAKIAFTGS 242

Query: 242 TPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEVC 301
           T  G  I + AA N+IP+T+ELGGKSPNIFF DIM+ + AF++KA EGLVL  FNQGEVC
Sbjct: 243 TSTGRVIAQAAANNLIPATLELGGKSPNIFFADIMDKDDAFLDKAIEGLVLFAFNQGEVC 302

Query: 302 TCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQ 361
           TCPSRA+IQESI++ FME V+K++ AIK  NPLDTD+M+GAQAS++Q  KILSY+++ +Q
Sbjct: 303 TCPSRAIIQESIYDQFMERVLKRVAAIKHQNPLDTDSMMGAQASKEQLTKILSYLDLGKQ 362

Query: 362 EGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEALA 421
           EGA++L GG    L G L  GYYVQPTL KGHNKMR+FQEEIFGPV+ V TFKDEAEALA
Sbjct: 363 EGAEVLAGGGQAHLGGDLEGGYYVQPTLFKGHNKMRIFQEEIFGPVLAVTTFKDEAEALA 422

Query: 422 IANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETH 481
           IANDT +GLGAGVW+R+ N AYRMGR IKAGRVWTNCYH YPAHAAFGGYK+SG+GRETH
Sbjct: 423 IANDTLYGLGAGVWSRNGNVAYRMGRAIKAGRVWTNCYHAYPAHAAFGGYKESGIGRETH 482

Query: 482 KMMLDHYQQTKNLLISYDINPLGFF 506
           KMMLDHYQQTKNLL+SY  N LGFF
Sbjct: 483 KMMLDHYQQTKNLLVSYSENKLGFF 507


Lambda     K      H
   0.319    0.136    0.406 

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: 760
Number of extensions: 24
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: 506
Length of database: 507
Length adjustment: 34
Effective length of query: 472
Effective length of database: 473
Effective search space:   223256
Effective search space used:   223256
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: 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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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, 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