GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudarthrobacter sulfonivorans Ar51

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_058929662.1 AU252_RS04330 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>NCBI__GCF_001484605.1:WP_058929662.1
          Length = 322

 Score =  140 bits (354), Expect = 5e-38
 Identities = 95/309 (30%), Positives = 160/309 (51%), Gaps = 16/309 (5%)

Query: 145 YVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGV 204
           Y + A GL +  G +GLL+ G   F AVGAY +A+ +  FG+ F+V L ++ I +A++ +
Sbjct: 22  YALAALGLAVHFGYSGLLNFGQAGFMAVGAYGFAISTLTFGVPFFVGLVIAVICSAIFAM 81

Query: 205 ILGFPVLRLRGDYLAIVTLAFGEIIRLVLI--NWTDVTKGTFGISSIPKATLFGIPFDAT 262
           +LG P LRLR DYLAIVT+A  EI+R ++     T VT    G+++         PF   
Sbjct: 82  LLGIPTLRLRADYLAIVTIAAAEIVRYIVTTNQLTAVTGSANGLAAFEGGFYAMNPF--P 139

Query: 263 AGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRS 322
           AG +  + +      + ++  + L++  C L       L R P GR  + +REDE A RS
Sbjct: 140 AGSYMGMNN---RDFFIRVVGWGLVIICCTLVWL----LMRSPWGRVLKGIREDENAVRS 192

Query: 323 LGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLT 382
           LG N    K+ A   G +    AG  F   +G V P ++    +  +   ++LGG+G++ 
Sbjct: 193 LGKNVYAYKMQALIMGGVLGALAGMIFTLPRGAVQPANYGTELTFFLYTCLLLGGLGTVL 252

Query: 383 GIAIAAIVMVGGTELLREMSFLKLIFGP-----DFTPELYRMLIFGLAMVVVMLFKPRGF 437
           G  I A++      L + + +  +  G             R ++ G+A++++M+F+P+G 
Sbjct: 253 GPVIGAMIFWVVLSLTQGILYGLIESGAVTWLNTVQAGQLRYILVGVALMLLMIFRPQGV 312

Query: 438 VGSREPTAF 446
            G+++  AF
Sbjct: 313 FGNKKELAF 321


Lambda     K      H
   0.330    0.145    0.432 

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: 457
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: 463
Length of database: 322
Length adjustment: 30
Effective length of query: 433
Effective length of database: 292
Effective search space:   126436
Effective search space used:   126436
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 (21.8 bits)
S2: 50 (23.9 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