GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Sinorhizobium meliloti 1021

Align Putative enoyl-CoA hydratase protein; EC 4.2.1.17 (characterized, see rationale)
to candidate SM_b21633 SM_b21633 enoyl-CoA hydratase

Query= uniprot:Q92VJ6
         (261 letters)



>FitnessBrowser__Smeli:SM_b21633
          Length = 263

 Score =  105 bits (262), Expect = 1e-27
 Identities = 80/266 (30%), Positives = 119/266 (44%), Gaps = 18/266 (6%)

Query: 4   DTIRCAIDQRGVARVTLARSEKHNALSATMIGELTAVVGRLATDASIRAVILDAEGKSFC 63
           DT+  A++  GV R+TL R +K NA +  M   L A   R  +D  +RAV+L   G+ F 
Sbjct: 5   DTVLSALEA-GVLRLTLNRPDKLNAFNEEMHLALRAGFERARSDDDVRAVMLTGAGRGFS 63

Query: 64  AGGDLDWMRQQFSADRPTRIAEATRLAM--------MLKALNDLPKPLIARVHGNAFGGG 115
           AG DL         DR  R   A  L          +L+ +  L KP++  V+G A G G
Sbjct: 64  AGQDL--------GDRDPRKGGAPDLGRTIETFYNPLLRLIRSLEKPVVCAVNGVAAGAG 115

Query: 116 VGLISVCDTVIAASGAQFGLTETRLGLIPATISPYVIAR-TGEARARPLFMSARVFGAEE 174
             +   CD  +AA  A+F     ++GL+P +   + + R  GEARA+ L M+A    AE 
Sbjct: 116 ANIAFACDITLAARSARFIQAFAKIGLVPDSGGTWSLPRLVGEARAKALAMTAEPLDAET 175

Query: 175 AKVAGFVTTVVDGTMLDGAVEAAVTAYLVAAPGAAGRAKRLARSLGLPITDAVIAATIEQ 234
           A   G +   VD   L     A             G  KR  ++      D  +    + 
Sbjct: 176 AASWGLIWRAVDDAALMDEASALAVRLAAGPTRGLGLTKRAIQAAATHSFDEQLDLERDL 235

Query: 235 LADTWETDEAREGVSAFFERRNPSWR 260
             +   + +  EGV+AF ++RNP +R
Sbjct: 236 QREAGRSADYAEGVTAFLDKRNPEFR 261


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: 173
Number of extensions: 11
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: 261
Length of database: 263
Length adjustment: 25
Effective length of query: 236
Effective length of database: 238
Effective search space:    56168
Effective search space used:    56168
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