GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Pseudomonas litoralis 2SM5

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_090272108.1 BLU11_RS03755 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_900105005.1:WP_090272108.1
          Length = 256

 Score =  268 bits (684), Expect = 1e-76
 Identities = 142/264 (53%), Positives = 188/264 (71%), Gaps = 9/264 (3%)

Query: 6   MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65
           M+  PLL V  L MRFGGL+AV+ V+     G+I ++IGPNGAGKTT+FNC+TGFY P+ 
Sbjct: 1   MSAAPLLDVSGLCMRFGGLLAVDQVALQVEEGQIVSLIGPNGAGKTTVFNCLTGFYKPSA 60

Query: 66  GRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRAS 125
           G +      G+E  +  MPG+++++   V RTFQ++RLF  MSV+ENL+VAQH+ +   +
Sbjct: 61  GSIRFH---GEE--VSGMPGFKLARMGMV-RTFQHVRLFKQMSVVENLLVAQHHHM---N 111

Query: 126 GFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCT 185
              +AGLL  PS+ R+E+EA+D A  WL+R  LLEFA+  AG L YG QRRLEIAR M T
Sbjct: 112 TNMLAGLLKTPSFRRSEKEALDRAAQWLERTGLLEFANRTAGTLAYGQQRRLEIARCMVT 171

Query: 186 EPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYG 245
           +P +L LDEPAAGLNPRE+ +L  L+  +R EH + +LLIEHDM +VM ISDHVVV++ G
Sbjct: 172 QPRLLMLDEPAAGLNPRETVDLQALIAELRSEHGLTILLIEHDMKLVMGISDHVVVINQG 231

Query: 246 RKISDGDPAFVKNDPAVIRAYLGE 269
             ++ G P  V  DP VI+AYLGE
Sbjct: 232 CPLAAGTPEQVCRDPEVIKAYLGE 255


Lambda     K      H
   0.319    0.137    0.397 

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: 214
Number of extensions: 7
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: 294
Length of database: 256
Length adjustment: 25
Effective length of query: 269
Effective length of database: 231
Effective search space:    62139
Effective search space used:    62139
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: 47 (22.7 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