GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bcd in Pseudomonas fluorescens FW300-N2C3

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate AO356_26355 AO356_26355 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26355 AO356_26355 acyl-CoA
           dehydrogenase
          Length = 375

 Score =  353 bits (906), Expect = e-102
 Identities = 176/372 (47%), Positives = 253/372 (68%)

Query: 6   TEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGLD 65
           TE+Q  I+DMA +FA++ L P   E D+ H + R+ I +M E GF G+  PE++GG    
Sbjct: 4   TEEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTG 63

Query: 66  VLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFGL 125
            L+Y + +EE++  D      +S + S+   PI  FG +EQK K+L P+A G  +GAF L
Sbjct: 64  YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123

Query: 126 TEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAFI 185
           TEP AG+DAS+ +T A L+GD Y+LNG K FIT+G+ A   +VFA+TD S G  GISAFI
Sbjct: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183

Query: 186 LEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRIG 245
           +    PG+   ++EDK+G H S T +++FE+ +VP  N LG+EGEG+KIA+  L+GGR+G
Sbjct: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVG 243

Query: 246 VAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAML 305
           +AAQA+G+A  A  AA  Y++ER  FG+ I + QA+ F +ADMAT+I  AR +V++AA L
Sbjct: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303

Query: 306 KNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEGT 365
           ++ G+P    A+MAK FAS++A +V + A+Q  GGYGY  D+P ER  R+ ++ QIYEGT
Sbjct: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363

Query: 366 NQVMRIVTSRAL 377
           + + R+V SR L
Sbjct: 364 SDIQRMVISRNL 375


Lambda     K      H
   0.318    0.134    0.379 

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: 369
Number of extensions: 13
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: 383
Length of database: 375
Length adjustment: 30
Effective length of query: 353
Effective length of database: 345
Effective search space:   121785
Effective search space used:   121785
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: 50 (23.9 bits)

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

Links

Downloads

Related tools

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:

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:

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:

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 preprint 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