GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Pseudomonas putida KT2440

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate PP_3492 PP_3492 short-chain acyl-CoA dehydrogenase

Query= metacyc::MONOMER-17424
         (375 letters)



>FitnessBrowser__Putida:PP_3492
          Length = 383

 Score =  441 bits (1133), Expect = e-128
 Identities = 215/373 (57%), Positives = 285/373 (76%)

Query: 3   VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62
           +++EQ  I D  R FA+  + P A+ W+K        + +M ELGL GM+VPE +GGS T
Sbjct: 6   LSEEQIMIRDMARDFARGEIAPHAQAWEKAGWIDDGVVRKMGELGLLGMVVPEDFGGSYT 65

Query: 63  GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122
            YVAYA+A+EEI+AG GA   +MS+HNSVGC P+L +G  +Q++Q+L  LA+G ++G F 
Sbjct: 66  DYVAYALAVEEISAGCGATGAMMSIHNSVGCGPLLAYGTAEQQQQWLPRLASGEVIGCFC 125

Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182
           LTEPQAGS+A +L+TRA L    +V+NG+KQF+++ + AG+ IVFAVTDPE GK+G+SAF
Sbjct: 126 LTEPQAGSEAHNLRTRAELVDGQWVINGAKQFVSNARRAGLAIVFAVTDPELGKKGLSAF 185

Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242
           +VPTD+PG++V R E K+G  ASDTC + FDN ++P AN LG  G+G  IAL+NLEGGRI
Sbjct: 186 LVPTDNPGFKVDRSEHKMGIRASDTCAVTFDNCRIPAANILGERGKGLAIALSNLEGGRI 245

Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302
           GIA+QA+G+ARAAFE A  Y+ +R  FGKP+ EHQ++A  LADM  +++ AR ++LHAA 
Sbjct: 246 GIAAQALGIARAAFEAALVYSRDRIQFGKPINEHQSIANLLADMQVQVNAARLLILHAAR 305

Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362
           LR AG+P L EAS AKLFASEMAE+VCS A+Q  GGYGYL D+P+ER YRD R+ QIYEG
Sbjct: 306 LRSAGKPCLSEASQAKLFASEMAERVCSMAIQVHGGYGYLEDYPVERYYRDARITQIYEG 365

Query: 363 TSDIQRMVIARNL 375
           +S+IQRM+IAR L
Sbjct: 366 SSEIQRMLIAREL 378


Lambda     K      H
   0.319    0.134    0.382 

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: 430
Number of extensions: 14
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: 375
Length of database: 383
Length adjustment: 30
Effective length of query: 345
Effective length of database: 353
Effective search space:   121785
Effective search space used:   121785
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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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:

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