Aligments for a candidate for gcdH in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for gcdH in Shewanella amazonensis SB2B

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__SB2B:6938693
          Length = 391

 Score =  561 bits (1446), Expect = e-164
 Identities = 278/391 (71%), Positives = 318/391 (81%), Gaps = 1/391 (0%)

Query: 2   VGKASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGE 61
           + +  F+W DPL  +  LTEEERM+RD  +++AQDKL  RVL A R E  D  I  E+GE
Sbjct: 1   MARVQFDWQDPLNFNSLLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGE 60

Query: 62  VGLLGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQK 121
           +GLLGAT+PE+YG +  NYV YGL+ARE+ER+DSGYRS MSVQSSLVM PI  +GTEAQ+
Sbjct: 61  LGLLGATLPEEYGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQR 120

Query: 122 QKYLPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFV 181
           +KYLPKLA+GEW+GCFGLTEP+ GSDP  M TRA ++DGGYR+TG+KMWITNSPIADVFV
Sbjct: 121 RKYLPKLATGEWVGCFGLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFV 180

Query: 182 VWAKDDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGL 241
           VWAK D G IRGFVLEKG +GLSAP I GK  LRASITGEIVMDNV V E+ + P+V GL
Sbjct: 181 VWAKLD-GAIRGFVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEDALLPNVEGL 239

Query: 242 KGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEI 301
           KGPF CLN ARYGI+WGALGAAE CWH ARQY LDR QF RPLAANQL QKKLADMQTEI
Sbjct: 240 KGPFGCLNKARYGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEI 299

Query: 302 TLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARH 361
           T  L  CL+ GR+ D     VE  S++KRNSCGKALDIAR+ARDM GGNGISDEF V RH
Sbjct: 300 TTGLFACLQAGRLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRH 359

Query: 362 LVNLEVVNTYEGTHDVHALILGRAQTGIQAF 392
           ++NLE VNTYEGTHD+HALILGRAQT +QAF
Sbjct: 360 VMNLEAVNTYEGTHDIHALILGRAQTDLQAF 390


Lambda     K      H
   0.320    0.137    0.413 

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: 524
Number of extensions: 17
Number of successful extensions: 2
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: 393
Length of database: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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