GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Corynebacterium deserti GIMN1.010

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter

Query= uniprot:A0A0C4YRF7
         (472 letters)



>NCBI__GCF_001277995.1:WP_082353324.1
          Length = 468

 Score =  422 bits (1084), Expect = e-122
 Identities = 211/441 (47%), Positives = 294/441 (66%), Gaps = 6/441 (1%)

Query: 19  LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78
           LHRGL +RH+Q+IAIGGAIG GLF+G+G+ I++AGP ++L YAI G  +FF+MRA+GELL
Sbjct: 11  LHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFVMRAMGELL 70

Query: 79  LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138
           L      S      + +GP AGF TGW+YWF W+ TGMA+I A+  Y  YW+P++P W+P
Sbjct: 71  LANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWWPEIPLWLP 130

Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIG--LAIIFFGVTPLGPTASF 196
            + T+ VL+ +N  AV +FGE+EFWFA+IK+V IVA+I +G  + I  FG  P G TASF
Sbjct: 131 GVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFG-APNGTTASF 189

Query: 197 SNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRIL 256
           +NL  HGGF P G  G +   QI +FA+ G+EL G  A E ++PE  LP A N +  RI+
Sbjct: 190 NNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAINSIPIRIV 249

Query: 257 IFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFS 316
           +FYV AL ++M + PWNE+ P  SPFV +F   G+P AA I+N VVIT+AASS NSGIFS
Sbjct: 250 VFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASSANSGIFS 309

Query: 317 TGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALM--GIGVLLNYIVPEQVFVWVTS 374
           T RMLY L+  G AP+ +G +S + VP+  +TFS   +   +G+L       + F  +T+
Sbjct: 310 TSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLYAGGTVIEAFTLITT 369

Query: 375 ISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLD 434
           +S V  +  WS I++A++ YR+       K+V F+MPG      +V+ F +A+  +LSL+
Sbjct: 370 VSSVLFMVVWSYILVAYIVYRRRNPELHEKSV-FKMPGGVVMAVVVLVFFVAMLGVLSLE 428

Query: 435 PGTRVALYVAPVWFALLGIGY 455
             TR AL   PVWF +LG+G+
Sbjct: 429 TDTRTALLATPVWFIILGVGW 449


Lambda     K      H
   0.328    0.142    0.445 

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: 747
Number of extensions: 34
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: 472
Length of database: 468
Length adjustment: 33
Effective length of query: 439
Effective length of database: 435
Effective search space:   190965
Effective search space used:   190965
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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 (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