GapMind for catabolism of small carbon sources

 

Aligments for a candidate for RR42_RS28305 in Burkholderia phytofirmans PsJN

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter

Query= uniprot:A0A0C4YRF7
         (472 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15500 BPHYT_RS15500 aromatic
           amino acid transporter
          Length = 461

 Score =  426 bits (1095), Expect = e-124
 Identities = 202/453 (44%), Positives = 304/453 (67%), Gaps = 5/453 (1%)

Query: 15  EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74
           ++  L RGLK+RHIQ+IA+GGAIG GLFLG+   +  AGP ++L YAIGG+  F IMR L
Sbjct: 6   QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMIMRQL 65

Query: 75  GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134
           GE++   PV+GSF+ +A ++ G F GF +GW+YW ++V+  MAE+TAV  Y+HYW+P VP
Sbjct: 66  GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVP 125

Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTA 194
            W+ AL   A++  +N   V  +GE EFWFA+IKVV ++ MIV G  ++  G    GP A
Sbjct: 126 TWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHG--GPQA 183

Query: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254
           S +NLW+HGGF P G  G+ + L ++MF++ G+ELIG+TA EA  P+K +P A N V++R
Sbjct: 184 SITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYR 243

Query: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314
           ILIFY+ +L ++++L PWNE+  G SPFV +F +IG    A ++N+VV+TAA S  NSG+
Sbjct: 244 ILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 303

Query: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374
           ++  RMLY LA+ G APRA  +V  + VP +AI  SA      V++NY++P +    + +
Sbjct: 304 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 363

Query: 375 ISLVGSLWTWSIIMIAHLGYRKA-IAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSL 433
           + +   +  W++I + HL  RKA +AAG  + + F+    P +NW+ +AFM  + V+L++
Sbjct: 364 LVVAALVLNWALISLTHLKSRKAMVAAG--ETLVFKSFWFPVSNWICLAFMALILVILAM 421

Query: 434 DPGTRVALYVAPVWFALLGIGYRFTKSRALLEG 466
            PG  V++++ P W  ++  GY F + RA ++G
Sbjct: 422 TPGLSVSVWLVPAWLVVMWAGYVFKRRRAAVQG 454


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: 740
Number of extensions: 33
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: 472
Length of database: 461
Length adjustment: 33
Effective length of query: 439
Effective length of database: 428
Effective search space:   187892
Effective search space used:   187892
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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