GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Stutzerimonas stutzeri A1501

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_011913061.1 PST_RS09700 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-11693
         (386 letters)



>NCBI__GCF_000013785.1:WP_011913061.1
          Length = 379

 Score =  275 bits (703), Expect = 2e-78
 Identities = 157/367 (42%), Positives = 227/367 (61%), Gaps = 7/367 (1%)

Query: 18  EFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGDYLALGIALEELA 77
           +FA + + P    +   H +P E + EM  +G FG+  PE++GG    YLA  +ALEE+A
Sbjct: 16  QFARERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTGYLAYAMALEEIA 75

Query: 78  RVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGLTEPDGGSDAGAT 137
             D + +  +    S+G +PI  FG D QK ++L  L  GE +GAF LTEP  GSDA + 
Sbjct: 76  AGDGACSTIMSVHNSVGCVPILRFGNDQQKRDFLGPLARGEQIGAFALTEPQAGSDASSL 135

Query: 138 RTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPD-GKPLISSIIVPSGTP 196
           RT AR D   + +V+NG K FIT+      G V V AVT   PD GK  IS+ IVP+ +P
Sbjct: 136 RTRARRDG--DHYVLNGAKQFITSGKH--AGTVIVFAVTD--PDAGKRGISAFIVPTDSP 189

Query: 197 GFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILDEGRIAISALAT 256
           G+ V     K+G +ASDT +++F D+RVP AN LGE+G GY   L  L+ GRI I+A A 
Sbjct: 190 GYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRIGIAAQAV 249

Query: 257 GLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWRDAASRLVAGEP 316
           G+A+   + +  YAGER  FG+ I  +QA+ F++ADM  +  +AR     AA+   AG P
Sbjct: 250 GMARAAFEAARDYAGERETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAALREAGRP 309

Query: 317 FKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILEIGEGTSEVQRM 376
              EA++AKL++S +A      A Q  GGYG+++++PV R++RD ++ +I EGTS++QR+
Sbjct: 310 ALVEASMAKLFASEMAERVCSAAIQTLGGYGYLSDFPVERIYRDVRVCQIYEGTSDIQRL 369

Query: 377 LIARELG 383
           +I+R LG
Sbjct: 370 VISRNLG 376


Lambda     K      H
   0.318    0.136    0.402 

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: 410
Number of extensions: 16
Number of successful extensions: 3
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: 386
Length of database: 379
Length adjustment: 30
Effective length of query: 356
Effective length of database: 349
Effective search space:   124244
Effective search space used:   124244
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 Apr 09 2024. 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