Alignments for a candidate for xylK_Tm in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Burkholderia phytofirmans PsJN

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS16930 BPHYT_RS16930 arabinose ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__BFirm:BPHYT_RS16930
          Length = 512

 Score =  396 bits (1017), Expect = e-114
 Identities = 217/501 (43%), Positives = 324/501 (64%), Gaps = 12/501 (2%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L+   I K FPGV A+D V F+V   ++  L+GENGAGKSTL+KIL G  +PD+G ++++
Sbjct: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
           G  V F S   +   GI+VIHQEL    ++TVAEN+ L      GQ       V++    
Sbjct: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLL------GQLPNSLGWVNKREAK 118

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
              +E L+ +G    P+A +R L+ AQRQMVEICKAL++  R+I +DEPTSSL+  ETE 
Sbjct: 119 RFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEV 178

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGE-FDVDTIIKMMV 253
           LF+++  L++   +++++SHR+DE+  + D   + RDG++I      E    DTI+  MV
Sbjct: 179 LFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMV 238

Query: 254 GREVEFFPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312
           GRE+    +    RP GE+    + ++     +  SFEVR+GE++GF GLVGAGR+E M 
Sbjct: 239 GREISDI-YNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMH 297

Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372
           LV+G + K+ G++ ++G+ +++++  +AI+ GI L PEDRK +G+V   TV +NI +   
Sbjct: 298 LVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCR 357

Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA-TNAD 431
           +   R G+ LD +KE E ++ ++K L IKTPS  Q    LSGGNQQK +L++WLA  +  
Sbjct: 358 RHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLK 417

Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491
           ++I DEPTRGIDVGAK EI+ +I +LA +G A++MISSELPE+L +SDRIVVM +G I+ 
Sbjct: 418 VVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISG 477

Query: 492 VLDNREKRVTQEEIMYYASGQ 512
            L  ++   T++ ++  A  Q
Sbjct: 478 ELTRKD--ATEQSVLSLALPQ 496



 Score = 90.9 bits (224), Expect = 1e-22
 Identities = 67/250 (26%), Positives = 114/250 (45%), Gaps = 12/250 (4%)

Query: 17  AKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGE 76
           AKGI     G        FEV   EIV   G  GAG+S L+ ++ G      GE+L++G+
Sbjct: 260 AKGI----EGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGK 315

Query: 77  RVEFHSPVDAFKKGISVI---HQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            ++  S  +A + GI +     +E  +    TV+ENI ++    R     +   +D    
Sbjct: 316 PIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINIS---CRRHYLRVGMFLDRKKE 372

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEP--RIIFMDEPTSSLTVEE 191
              +   + L+  K           +   Q   I    + EP  +++ +DEPT  + V  
Sbjct: 373 AETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGA 432

Query: 192 TERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKM 251
              ++ +I  L  RG ++V +S  L EV+ +SDRIVVMR G+  GEL + +    +++ +
Sbjct: 433 KHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSL 492

Query: 252 MVGREVEFFP 261
            + +     P
Sbjct: 493 ALPQSSTALP 502


Lambda     K      H
   0.319    0.138    0.381 

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: 700
Number of extensions: 38
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 520
Length of database: 512
Length adjustment: 35
Effective length of query: 485
Effective length of database: 477
Effective search space:   231345
Effective search space used:   231345
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources