Alignments for a candidate for acdH in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acdH in Shewanella loihica PV-4

Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate 5209191 Shew_1669 butyryl-CoA dehydrogenase (RefSeq)

Query= reanno::ANA3:7025618
         (385 letters)



>FitnessBrowser__PV4:5209191
          Length = 385

 Score =  705 bits (1819), Expect = 0.0
 Identities = 349/385 (90%), Positives = 365/385 (94%)

Query: 1   MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60
           MDFN NEDQRQFA+LA QFA +ELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG
Sbjct: 1   MDFNLNEDQRQFAELATQFAQEELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60

Query: 61  GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120
           GMGLSRLD+SIIFE+L+ GCTATTAMLTIHNMATWMVT++G+ TLR  WSE LTTG  LA
Sbjct: 61  GMGLSRLDSSIIFEQLAMGCTATTAMLTIHNMATWMVTSFGSQTLRDEWSEALTTGNKLA 120

Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGIS 180
           SYCLTE GAGSDAASL+TKAVREGDEYV+SG+KMFISGAGSTELLVVMCRTG AGPKGIS
Sbjct: 121 SYCLTEAGAGSDAASLKTKAVREGDEYVISGAKMFISGAGSTELLVVMCRTGDAGPKGIS 180

Query: 181 AIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGG 240
           AIAIPAD+ GI YGKAEDKMGWNAQPTR +TFD VRVPV NLLGEEGQGFTFAMKGLDGG
Sbjct: 181 AIAIPADAAGISYGKAEDKMGWNAQPTREITFDKVRVPVTNLLGEEGQGFTFAMKGLDGG 240

Query: 241 RINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLA 300
           RINIATCSVGTAQAALERA QYMNERQQFGKP+AAFQALQFKLADMATELVAARQMVRLA
Sbjct: 241 RINIATCSVGTAQAALERAQQYMNERQQFGKPIAAFQALQFKLADMATELVAARQMVRLA 300

Query: 301 AFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQI 360
           AFKLDSGDPEATAYCAMAKRFATDVGF VCD+ALQ+HGGYGYIREYPLERHFRDVRVHQI
Sbjct: 301 AFKLDSGDPEATAYCAMAKRFATDVGFNVCDSALQLHGGYGYIREYPLERHFRDVRVHQI 360

Query: 361 LEGTNEIMRLIIARRLLDENAGQIL 385
           LEGTNEIMRLIIARRLLDENA QIL
Sbjct: 361 LEGTNEIMRLIIARRLLDENASQIL 385


Lambda     K      H
   0.320    0.134    0.396 

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: 587
Number of extensions: 5
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: 385
Length of database: 385
Length adjustment: 30
Effective length of query: 355
Effective length of database: 355
Effective search space:   126025
Effective search space used:   126025
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: 50 (23.9 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