GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Corynebacterium deserti GIMN1.010

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

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>NCBI__GCF_001277995.1:WP_082353324.1
          Length = 468

 Score =  335 bits (860), Expect = 1e-96
 Identities = 169/447 (37%), Positives = 260/447 (58%), Gaps = 5/447 (1%)

Query: 2   DNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMI 61
           DNA     L RGL NRH+QLIA+GGAIGTGLF+GS   +  AGPS+IL YAI G + F +
Sbjct: 3   DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62

Query: 62  MRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWW 121
           MR +GE++       S         G   GF++GW YW  ++   MA++ A+  Y  YWW
Sbjct: 63  MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122

Query: 122 PGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGP 181
           P +P W+  ++    + A+NLA V+ +GE EFWFAIIK+VA++ +I  G +++++  G P
Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAP 182

Query: 182 Q---ASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVN 238
               AS +NL  HGGFFP+G  G      + +F+F G+EL G  AAE  +P+ ++P+A+N
Sbjct: 183 NGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAIN 242

Query: 239 QVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSV 298
            +  RI++FY+ +LAV++ + PWNEV+   SPFV +F+  G    A ++N VV+T+A S 
Sbjct: 243 SIPIRIVVFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASS 302

Query: 299 YNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYL--IPAE 356
            NSG+++ SRMLYGL+ +G AP+    + +R VP   +  S L     V + Y      E
Sbjct: 303 ANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLYAGGTVIE 362

Query: 357 ALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALIL 416
           A  L+  +     ++ W+ I + ++  RR      E  VFK     V   + L F   +L
Sbjct: 363 AFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVVVLVFFVAML 422

Query: 417 VILAMTPGLSVSVLLVPLWLVVMWAGY 443
            +L++      ++L  P+W +++  G+
Sbjct: 423 GVLSLETDTRTALLATPVWFIILGVGW 449


Lambda     K      H
   0.327    0.140    0.440 

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: 512
Number of extensions: 24
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: 461
Length of database: 468
Length adjustment: 33
Effective length of query: 428
Effective length of database: 435
Effective search space:   186180
Effective search space used:   186180
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: 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