GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Paraburkholderia bryophila 376MFSha3.1

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>FitnessBrowser__Burk376:H281DRAFT_01668
          Length = 459

 Score =  289 bits (739), Expect = 2e-82
 Identities = 150/446 (33%), Positives = 249/446 (55%), Gaps = 2/446 (0%)

Query: 5   LQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQ 64
           +Q   LK+ LK RHI +IALGG IG GLF+GS S++  AGP+ IL Y IGGV+  ++M  
Sbjct: 1   MQDYSLKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFM 60

Query: 65  LGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGV 124
           LGEM ++ P +GSFS +A  Y G++ GF  GW YW   ++    E   +G  +H + P +
Sbjct: 61  LGEMASRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWL 120

Query: 125 PTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGG-PQA 183
           P    AL     + A N  +V+A+GE E+W +  KV  +I  ++ G  +L     G P  
Sbjct: 121 PVPAGALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGLQPGIPAP 180

Query: 184 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 243
            + NL  HGGF P+G   + + + V++FS GG E+  + A E++ P K++ +A+  VI R
Sbjct: 181 GLLNLTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILR 240

Query: 244 ILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 303
           +++FY+ S+++L+   PW + A   SP+V +FS  G T  A  + +V+  + +SV NS +
Sbjct: 241 VMVFYVGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFL 300

Query: 304 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 363
           ++NSRML+ L+++G+AP    + + +GVP  A+ L  +   + + +++L   +   +L  
Sbjct: 301 FSNSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFLMLAK 360

Query: 364 LVVAALVLNWALISLTHLKSRR-AMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMT 422
              A +++ W  I + H   RR       +   F+++++PVSNW+ L  +  +L   A  
Sbjct: 361 SSGAFVMIVWIFIIVAHFAMRRQTKHEQRDPASFRAWFYPVSNWVALLALVAVLGSQAFN 420

Query: 423 PGLSVSVLLVPLWLVVMWAGYAFKRR 448
           P             + + A Y  +RR
Sbjct: 421 PESRFQFWFAVSTALAIVAWYYVRRR 446


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: 480
Number of extensions: 25
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: 461
Length of database: 459
Length adjustment: 33
Effective length of query: 428
Effective length of database: 426
Effective search space:   182328
Effective search space used:   182328
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 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:

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