GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Pseudarthrobacter sulfonivorans Ar51

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_058929662.1 AU252_RS04330 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A159ZYE0
         (418 letters)



>NCBI__GCF_001484605.1:WP_058929662.1
          Length = 322

 Score =  153 bits (387), Expect = 6e-42
 Identities = 95/304 (31%), Positives = 154/304 (50%), Gaps = 33/304 (10%)

Query: 123 YVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGF 182
           Y +  LGL +  G +GLL+ G  GF AVGAY +A+ +  FG+ F++ L IA + +A F  
Sbjct: 22  YALAALGLAVHFGYSGLLNFGQAGFMAVGAYGFAISTLTFGVPFFVGLVIAVICSAIFAM 81

Query: 183 LLGFPVLRLRGDYLAIVTLGFGEIIRLFL--RNLTDITGGPNGISNIEKPTFFGLTFERK 240
           LLG P LRLR DYLAIVT+   EI+R  +    LT +TG  NG++  E   +    F   
Sbjct: 82  LLGIPTLRLRADYLAIVTIAAAEIVRYIVTTNQLTAVTGSANGLAAFEGGFYAMNPFPAG 141

Query: 241 AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI 300
           +  G+              N+  F+ +V   L +    ++  L+R P GR  + +REDE 
Sbjct: 142 SYMGMN-------------NRDFFIRVVGWGLVIICCTLVWLLMRSPWGRVLKGIREDEN 188

Query: 301 ACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 360
           A R+LG N    K+ A  +G      AG  F   +G V P ++    +  +   ++LGG+
Sbjct: 189 AVRSLGKNVYAYKMQALIMGGVLGALAGMIFTLPRGAVQPANYGTELTFFLYTCLLLGGL 248

Query: 361 GSQLGVILAAIVMILLPEMMR------------------EFSEYRMLMFGALMVLMMIWR 402
           G+ LG ++ A++  ++  + +                  +  + R ++ G  ++L+MI+R
Sbjct: 249 GTVLGPVIGAMIFWVVLSLTQGILYGLIESGAVTWLNTVQAGQLRYILVGVALMLLMIFR 308

Query: 403 PQGL 406
           PQG+
Sbjct: 309 PQGV 312


Lambda     K      H
   0.331    0.145    0.439 

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: 437
Number of extensions: 32
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: 418
Length of database: 322
Length adjustment: 30
Effective length of query: 388
Effective length of database: 292
Effective search space:   113296
Effective search space used:   113296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 49 (23.5 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