GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21105 in Pseudovibrio axinellae Ad2

Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate WP_068002934.1 PsAD2_RS04495 carbohydrate ABC transporter permease

Query= reanno::Smeli:SM_b21105
         (288 letters)



>NCBI__GCF_001623255.1:WP_068002934.1
          Length = 290

 Score =  164 bits (416), Expect = 2e-45
 Identities = 79/206 (38%), Positives = 129/206 (62%), Gaps = 2/206 (0%)

Query: 84  NSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYA- 142
           NSLIV + ST + L IG    YA  R++F  +  + +G +L R VP   L +P+F ++  
Sbjct: 86  NSLIVGLLSTGLTLTIGCMAAYALVRFQFMGRGTVSMGTLLMRIVPPAVLLVPVFGIWTF 145

Query: 143 RTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPL 202
           + G+  T+  +IL Y A+N+PF IW++  F  QVP  L EAA++DG  P+Q F+ V  P+
Sbjct: 146 QYGLDQTYAGIILIYTAMNLPFVIWILQSFIVQVPIQLEEAARMDGANPFQVFFLVVLPI 205

Query: 203 AGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAVVM 262
             PG+A+A IF F  +WNE+ LA+ ++   +++T PV +++   E+ IDW  + A  +++
Sbjct: 206 IQPGLAAAAIFTFRIAWNEFLLANALS-GRSTRTAPVTIVNSITEYDIDWGVIMATGMLL 264

Query: 263 IVPALTLTFIIQKHLVSGLTFGAVKG 288
            +P +  TF+  K +++G+T GAVKG
Sbjct: 265 AIPPILFTFVASKQIITGMTAGAVKG 290


Lambda     K      H
   0.328    0.141    0.442 

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: 240
Number of extensions: 12
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: 288
Length of database: 290
Length adjustment: 26
Effective length of query: 262
Effective length of database: 264
Effective search space:    69168
Effective search space used:    69168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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