GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Pseudarthrobacter sulfonivorans Ar51

Align ABC transporter permease (characterized, see rationale)
to candidate WP_058929184.1 AU252_RS01305 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>NCBI__GCF_001484605.1:WP_058929184.1
          Length = 288

 Score =  141 bits (356), Expect = 2e-38
 Identities = 95/309 (30%), Positives = 166/309 (53%), Gaps = 24/309 (7%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MD L+Q  +NGL LG+ YAL+ALG+++V+G++ +INFAHG   ++G   ++S   +M G 
Sbjct: 1   MDTLVQATVNGLALGAQYALLALGFSLVFGVLGVINFAHGAFYVLGGYFTYS---LMTGL 57

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120
             G P      LA I A +  A + +V+E +    +  +     LI ++G   ++     
Sbjct: 58  --GLP----YALALIAAVLGVAAVGYVMELLLIEKIVDNHE-GTLIVSLGFYFVVIAALT 110

Query: 121 IIWKPNYKPYPTMLP-SSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179
           + + P  +  P   P  S   + G +I   +++++ V+AVA+  L +L+  +  G A+RA
Sbjct: 111 LFYGP--EAVPVRFPVDSVLRLEGFYIPVARLIVIAVSAVAVLGLWFLLYRSKHGIALRA 168

Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239
            +EN  VA++ G++P +       + A LA +AG +    + T +  +G    + +F   
Sbjct: 169 LSENRDVATMQGLRPRVYFPLAVALSAALAGLAGGLVTPIF-TLEPPVGEAALMVSFLVV 227

Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYI-GTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298
           V GG+G+L GA    + +GL+EAI   Y+ G+LT  LL         F++++ +L  RPS
Sbjct: 228 VLGGLGSLVGAASAAVGVGLVEAIAGTYLDGSLTRLLL---------FVIVLALLLFRPS 278

Query: 299 GLLGERVAD 307
           G+ G  + D
Sbjct: 279 GIAGRSLRD 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: 200
Number of extensions: 8
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: 309
Length of database: 288
Length adjustment: 27
Effective length of query: 282
Effective length of database: 261
Effective search space:    73602
Effective search space used:    73602
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 Apr 09 2024. 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