GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Acidovorax sp. GW101-3H11

Align ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_1939 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= uniprot:A0A165KC95
         (309 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1939 High-affinity
           branched-chain amino acid transport system permease
           protein LivH (TC 3.A.1.4.1)
          Length = 291

 Score =  154 bits (388), Expect = 3e-42
 Identities = 99/307 (32%), Positives = 171/307 (55%), Gaps = 29/307 (9%)

Query: 5   LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64
           +Q +I+G+  G +Y LIALG+ ++Y   + ++FA GE++M+GA    + + ++     G 
Sbjct: 4   VQLLISGVSQGCIYGLIALGFVLIYKATETVSFAQGELMMLGAFCGLALMTVL-----GF 58

Query: 65  PGWVILLLATIIACVVAATL-NFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123
           P WV      ++A VVA  L   ++E+   RP+   P  + ++  IG+  +L+ L  +I 
Sbjct: 59  PFWV-----AVLASVVAMGLFGVLVERAVIRPILGQPAFSIVMLTIGIGYVLRGLVTMI- 112

Query: 124 KPNYKPYPTMLP----SSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179
            PN       LP         +G   ++  Q++++G T      L  +  ++ LG AM+A
Sbjct: 113 -PNIGTDTHTLPVPYKDQSLRLGELVVSAEQLVVIGATGALCVLLFAMFRYSKLGIAMQA 171

Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHT-MGFLPGLKAFTA 238
            ++N   A  MG+    +    + + AV+AA+AG++ A    T  H  MGF+ GLKAF A
Sbjct: 172 ASQNQLAAYYMGIPVQRLNGLAWGLAAVVAAVAGLLLAPI--TFVHANMGFI-GLKAFPA 228

Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298
           AV GG G+L GA+VGG+++G++E        +L+G  L   + D  A+IV++I+L ++P+
Sbjct: 229 AVVGGFGSLPGAIVGGLVIGIVE--------SLSGFYLPDGFKDTAAYIVVLIMLMVKPN 280

Query: 299 GLLGERV 305
           GL GE++
Sbjct: 281 GLFGEKL 287


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: 213
Number of extensions: 12
Number of successful extensions: 5
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: 291
Length adjustment: 27
Effective length of query: 282
Effective length of database: 264
Effective search space:    74448
Effective search space used:    74448
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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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