GapMind for catabolism of small carbon sources

 

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

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

Query= uniprot:Q4KIP0
         (466 letters)



>NCBI__GCF_001277995.1:WP_082353324.1
          Length = 468

 Score =  347 bits (890), Expect = e-100
 Identities = 187/467 (40%), Positives = 274/467 (58%), Gaps = 15/467 (3%)

Query: 2   DQTLKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 61
           D       L RGL NRH+QLIA+GGAIGTGLF+GS   +  AGPS+IL YAI GF+ F +
Sbjct: 3   DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62

Query: 62  MRQLGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWW 121
           MR +GE+++      S         G   GF+ GW YW  ++  GMA++ A+  Y Q+WW
Sbjct: 63  MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122

Query: 122 PEIPTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYML---FSGS 178
           PEIP W+   +  +++  +N+  V+ FGE EFWFAIIK+VAIV +I +G +M+   F   
Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAP 182

Query: 179 GGSQASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAIN 238
            G+ AS +NL  HGGFFPNG TG L      +F+F G+EL G  AAE  +P   +P+AIN
Sbjct: 183 NGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAIN 242

Query: 239 QVVYRVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNF 298
            +  R+++FYV ALAV++ + PW+E+         +  +SPFV++F+L G  AAA I+NF
Sbjct: 243 SIPIRIVVFYVLALAVIMMVTPWNEV---------SPDNSPFVQMFALAGIPAAAGIINF 293

Query: 299 VVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLV 358
           VV+T+A S  NSG++  SRMLYGL+ +G APK    L+K+ VP   L  S L  +  V +
Sbjct: 294 VVITSAASSANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGL 353

Query: 359 NYLAPH--EALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYL 416
            Y      EA  L+  +     M+ W+ I + ++ +R+   E      FK     +   +
Sbjct: 354 LYAGGTVIEAFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVV 413

Query: 417 CLAFMVMIVGVMWMIPGIRASVYAIPVWVLVIW-GFYLLSRAKKASQ 462
            L F V ++GV+ +    R ++ A PVW +++  G++    AK A +
Sbjct: 414 VLVFFVAMLGVLSLETDTRTALLATPVWFIILGVGWFATGGAKGAQR 460


Lambda     K      H
   0.327    0.141    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: 654
Number of extensions: 40
Number of successful extensions: 5
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: 466
Length of database: 468
Length adjustment: 33
Effective length of query: 433
Effective length of database: 435
Effective search space:   188355
Effective search space used:   188355
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