GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17590 in Chromobacterium vaccinii MWU205

Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate WP_046158297.1 VL52_RS17825 ABC transporter substrate-binding protein

Query= uniprot:A0A1N7UK26
         (258 letters)



>NCBI__GCF_000971335.1:WP_046158297.1
          Length = 254

 Score =  166 bits (420), Expect = 4e-46
 Identities = 96/256 (37%), Positives = 149/256 (58%), Gaps = 10/256 (3%)

Query: 5   RSLFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEV 64
           ++L A+  + L A+  AQ  + +R GV   YPPF    ADG  QGFDI++ N++CA ++V
Sbjct: 3   KALIASAGIALLASLSAQA-ETLRIGVDLNYPPFSKQGADGKPQGFDIDIANSLCAAMKV 61

Query: 65  KCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFG 124
            C  V  ++DG+IPAL A KFDAI+SSM +TP R+K +DFS + +    ++ +R  A  G
Sbjct: 62  TCQIVPQDWDGLIPALNANKFDAIISSMQITPERQKAVDFSHKYY----NIASRMVAKDG 117

Query: 125 DTPE--SLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTD 182
              +  SL GK++GVL+ S QE +A+ +  K GA I +Y    +++ DL++GR+DA   D
Sbjct: 118 TKVDAASLKGKKIGVLRASTQEKFAKDNWGKNGAAIVSYAKSPESFLDLKSGRVDAVFVD 177

Query: 183 KLEAQLNFLSKPEGSDFK-TGPAFKD-PTLPLDIAMGLRKNDQALRALINKGIAAVQADG 240
               +  FL   +   +   GP + D         + ++K ++AL   +NK I  ++ DG
Sbjct: 178 SAVGEQEFLKTAQAKGYAFVGPNYSDVKYFGPGCGIAVKKGNKALVERLNKAIDQIRKDG 237

Query: 241 TYAQIQKKYFGDQDIY 256
            Y ++Q KYF   DIY
Sbjct: 238 AYKKVQDKYF-SFDIY 252


Lambda     K      H
   0.319    0.135    0.393 

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: 171
Number of extensions: 9
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: 258
Length of database: 254
Length adjustment: 24
Effective length of query: 234
Effective length of database: 230
Effective search space:    53820
Effective search space used:    53820
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