GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Burkholderia phytofirmans PsJN

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate BPHYT_RS31715 BPHYT_RS31715 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>FitnessBrowser__BFirm:BPHYT_RS31715
          Length = 380

 Score =  229 bits (583), Expect = 1e-64
 Identities = 136/366 (37%), Positives = 196/366 (53%), Gaps = 8/366 (2%)

Query: 4   KLSLLVAVAATAMTASVAKADIAV---ATAGPITGQYATFGEQMKKGIEQAVADINAAGG 60
           K    VA  + A  A+ A  DI V    +A P TG  A  G++ + G   AV D+N  G 
Sbjct: 6   KHGFAVAALSAACNAAFAADDITVIKIGSAAPTTGAIANLGKENENGARLAVEDVNRRGL 65

Query: 61  VL-GQKLKLEVG--DDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVL 117
           V+ G+K+KLE+   DD  DP+Q   VA +L   GV  V GH  SG SI AS++Y +  +L
Sbjct: 66  VINGKKIKLELDAVDDQADPRQGTQVAQRLVDDGVVAVVGHLNSGVSIAASRIYHDAQIL 125

Query: 118 QISPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLA 177
           QISP STNPK T+Q     +R+   D QQ  +   Y LE  K K VAI+ D +AYG+GLA
Sbjct: 126 QISPDSTNPKFTQQGFNTTYRLVATDAQQSPVLAHYALETLKAKKVAIVDDSTAYGQGLA 185

Query: 178 DETQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKD 237
           D+   A+ +GG      EA      D+  +++K+K ++ DV++ GG    AG   +Q+  
Sbjct: 186 DQFSSAVKSGGATVVAREATNDKTIDFKGVITKIKGQSPDVIFYGGMDATAGPFIKQVAQ 245

Query: 238 QGLNAPIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEK--FRKAGYEPE 295
            GLNA ++ GD   ++E  A+ GPA +  + +    P    +A  A EK   ++ G   +
Sbjct: 246 LGLNAKVLGGDGTCSDEVIALAGPAVDRLVCSIAGLPLSRMKAGPAFEKEYQQRFGMPVQ 305

Query: 296 GYTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWY 355
            Y  Y Y A+ +  +A K++ STD AKI        Y  + G+I FD KGDV SP    Y
Sbjct: 306 IYAPYAYDAVMVIVDAMKKSGSTDHAKILAAASATDYQGLTGQIQFDDKGDVRSPRLTLY 365

Query: 356 RWNNGQ 361
            + +G+
Sbjct: 366 GYKDGK 371


Lambda     K      H
   0.312    0.129    0.366 

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: 333
Number of extensions: 18
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: 366
Length of database: 380
Length adjustment: 30
Effective length of query: 336
Effective length of database: 350
Effective search space:   117600
Effective search space used:   117600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 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