GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Burkholderia phytofirmans PsJN

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS15600 BPHYT_RS15600 ABC transporter ATP-binding protein

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__BFirm:BPHYT_RS15600
          Length = 389

 Score =  444 bits (1143), Expect = e-129
 Identities = 224/353 (63%), Positives = 275/353 (77%), Gaps = 3/353 (0%)

Query: 1   MKNTKTNWIIGAVALLVLPLILQSFG-NAWVRIADLALLYVLLALGLNIVVGYAGLLDLG 59
           +  T T  II A+ ++  P+I+ + G N WVR+ D A+LYV+LALGLN+VVG+AGLLDLG
Sbjct: 19  LTKTLTVGIITAIFVIAAPMIIGAAGGNYWVRVLDFAMLYVMLALGLNVVVGFAGLLDLG 78

Query: 60  YVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAP 119
           Y+AFYAVGAY  AL++SPHL+  F   A + PNGLH    I++P A  +AAFFG +LGAP
Sbjct: 79  YIAFYAVGAYTSALLSSPHLSSQFEWIAHLAPNGLHVPFLIIVPCAMAVAAFFGVILGAP 138

Query: 120 TLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVF 179
           TL+LRGDYLAIVTLGFGEI+RIFLNNLD PVN+TNGPKG+  ID V      L +   +F
Sbjct: 139 TLRLRGDYLAIVTLGFGEIVRIFLNNLDRPVNITNGPKGITGIDPVHAGDFSLAQTHSLF 198

Query: 180 GFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLL 239
           G    SV  YYYLF++  ++ + +C RLQ SRIGRAW AIREDEIAAKAMGINTRN+KLL
Sbjct: 199 GLQFPSVYSYYYLFVLAALLVIWVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVKLL 258

Query: 240 AFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSA 299
           AF MGASFGG+SGAMFG+FQGFVSPESF+L ES++++A VVLGG+GHIPGVILGAVLL+ 
Sbjct: 259 AFAMGASFGGLSGAMFGSFQGFVSPESFTLPESIVVLACVVLGGMGHIPGVILGAVLLAV 318

Query: 300 LPEVLRYVAGPLQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEH 350
           LPE LR   GPLQ M  G   +D+ ++RQL+ ALAM++IML R  GLWPSP+H
Sbjct: 319 LPEFLRSTMGPLQNMVFGHEIVDTEVIRQLVYALAMVLIMLYRSEGLWPSPKH 371


Lambda     K      H
   0.328    0.144    0.430 

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: 457
Number of extensions: 17
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: 358
Length of database: 389
Length adjustment: 30
Effective length of query: 328
Effective length of database: 359
Effective search space:   117752
Effective search space used:   117752
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: 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