GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter permease (characterized, see rationale)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein

Query= uniprot:A0A165KC95
         (309 letters)



>MicrobesOnline__882:208249
          Length = 306

 Score =  199 bits (507), Expect = 5e-56
 Identities = 114/307 (37%), Positives = 175/307 (57%), Gaps = 13/307 (4%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           M+  +Q I N L  GS YALIALGYT+VYG++ LINFAHG++ M+GA  S+    ++ G 
Sbjct: 1   METFIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFVASILLGQ 60

Query: 61  MPG---APGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILL 115
           + G     G + L L   +  V+ A +   +E+VAYRPLR   + RL  +ITA+   I+L
Sbjct: 61  IGGFFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIML 120

Query: 116 QTLAMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGR 175
           +   + +   + K  P M+    + IG   +T  +++++    +  A L ++V  T +G 
Sbjct: 121 ENGNLALLGASRKALPEMIDKVVYTIGTVSVTNLKLMVIVTAFLVFALLQFIVTRTRIGM 180

Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235
           AMRA A +     LMG+  D +I  TF++G+  A +AG+++A +Y      MG + G KA
Sbjct: 181 AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA 240

Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295
           F AAV GGIG++ GA +GG LL  IE         +   +  S + D+FAF +L+ I+  
Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIE--------IMVAAVFPSTFRDLFAFSILLFIMWQ 292

Query: 296 RPSGLLG 302
           RP+GL G
Sbjct: 293 RPTGLFG 299


Lambda     K      H
   0.327    0.142    0.419 

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: 224
Number of extensions: 13
Number of successful extensions: 4
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: 309
Length of database: 306
Length adjustment: 27
Effective length of query: 282
Effective length of database: 279
Effective search space:    78678
Effective search space used:    78678
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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