GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Phaeobacter inhibens BS107

Align Putative enoyl-CoA hydratase protein; EC 4.2.1.17 (characterized, see rationale)
to candidate GFF1019 PGA1_c10360 putative enoyl-CoA hydratase

Query= uniprot:Q92VJ6
         (261 letters)



>FitnessBrowser__Phaeo:GFF1019
          Length = 260

 Score =  283 bits (724), Expect = 3e-81
 Identities = 149/259 (57%), Positives = 174/259 (67%)

Query: 3   FDTIRCAIDQRGVARVTLARSEKHNALSATMIGELTAVVGRLATDASIRAVILDAEGKSF 62
           ++TI  AID RGVA +TL R EKHNA+S  M+ EL A    LA D ++R V+L   GKSF
Sbjct: 2   YNTITLAIDDRGVATLTLNRPEKHNAMSGEMLQELKAAAAALAKDRTVRVVVLTGAGKSF 61

Query: 63  CAGGDLDWMRQQFSADRPTRIAEATRLAMMLKALNDLPKPLIARVHGNAFGGGVGLISVC 122
           CAGGDL WM+ Q  AD  TR  EA  LA ML A+N LP+P+I  + GNAFGGGVG+ SVC
Sbjct: 62  CAGGDLGWMQAQMEADAETRGREARVLAEMLMAINTLPQPVIGAIQGNAFGGGVGMASVC 121

Query: 123 DTVIAASGAQFGLTETRLGLIPATISPYVIARTGEARARPLFMSARVFGAEEAKVAGFVT 182
           D  I A   + GLTETRLGLIPATI PYV+AR GEARAR +FMSAR+FGA EA   G + 
Sbjct: 122 DVAIGADHIKMGLTETRLGLIPATIGPYVVARMGEARARRVFMSARLFGAAEAVDLGILA 181

Query: 183 TVVDGTMLDGAVEAAVTAYLVAAPGAAGRAKRLARSLGLPITDAVIAATIEQLADTWETD 242
            VV    LD A+EA V  YL  AP A G AK L R LG  I DAVI  TI  L D WE  
Sbjct: 182 RVVPAADLDAAIEAEVIPYLSCAPEAVGAAKALVRDLGPKIDDAVIDHTIAALVDRWEGS 241

Query: 243 EAREGVSAFFERRNPSWRQ 261
           EA EG++AFF +  PSW++
Sbjct: 242 EAPEGIAAFFAKEKPSWQR 260


Lambda     K      H
   0.321    0.133    0.383 

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: 208
Number of extensions: 9
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: 261
Length of database: 260
Length adjustment: 25
Effective length of query: 236
Effective length of database: 235
Effective search space:    55460
Effective search space used:    55460
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 (21.9 bits)
S2: 47 (22.7 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