Alignments for a candidate for rbsA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Burkholderia phytofirmans PsJN

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__BFirm:BPHYT_RS20740
          Length = 503

 Score =  456 bits (1172), Expect = e-132
 Identities = 244/494 (49%), Positives = 328/494 (66%), Gaps = 3/494 (0%)

Query: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60
           M  L+ +K + K FPGV+AL      +  G V AL+GENGAGKST+MK+L G+YTRD G 
Sbjct: 1   MTPLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGE 60

Query: 61  LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGK-IDWKTMY 119
           +L+ G+   F  P+ +Q  G+GIIHQEL L+  LTIA+N+F+GRE   R G  +D   + 
Sbjct: 61  ILYEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLN 120

Query: 120 AEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETES 179
           A+A  +LA++++      LV  L++  QQMVEIAK LSF+S+V+IMDEPT AL D E   
Sbjct: 121 AQAHDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAE 180

Query: 180 LFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG 239
           LFR+IR+LK +G GI+YISH+M E+ +I D VTV RDG+++A   V   T  ++I MMVG
Sbjct: 181 LFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVG 240

Query: 240 RKLEDQYPHLDKA-PGDIRLKVDNL-CGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKV 297
           R L D  P    A  G++ L+V  L  GP V DVSF LRKGEILG +GLMGAGRTE+ + 
Sbjct: 241 RTLTDAAPSQHIANQGEVALEVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRTEVARA 300

Query: 298 LYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALR 357
           ++GA P  SG + + G +   R+P D +A GI Y+SEDRKR GL  GMSV+ N+ ++ LR
Sbjct: 301 VFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNLR 360

Query: 358 YFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVL 417
            F      L+    ++  + FI L  ++TPS  Q + LLSGGNQQK+ IA+ L     VL
Sbjct: 361 KFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCDVL 420

Query: 418 ILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEF 477
             DEPTRG+DVGAK EIY+L+      G +I+++SSE+PE+L MSDRI+VM EG ++GE 
Sbjct: 421 FFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITGEL 480

Query: 478 TREQATQEVLMAAA 491
               ATQE +M  A
Sbjct: 481 AAAGATQERIMQLA 494



 Score = 92.4 bits (228), Expect = 3e-23
 Identities = 65/232 (28%), Positives = 115/232 (49%), Gaps = 8/232 (3%)

Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV   ++V F L  GE+  + G  GAG++ LMK+L G   R +G +  +G  V  +SP+
Sbjct: 15  PGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILYEGQPVDFQSPR 74

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382
           +  A G+  I ++ +   L+  +++ +NM +       R G  L          D +   
Sbjct: 75  EAQAVGVGIIHQELQ---LMNHLTIAQNMFI-GREPRGRLGLFLDEDKLNAQAHDILARM 130

Query: 383 NVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFK 442
           +V T      +  L+   QQ V IA+ L    +VLI+DEPT  ++     E++++I   K
Sbjct: 131 HV-TLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFRIIRDLK 189

Query: 443 ADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
             G+ II +S +M E+  ++DR+ V+ +G        +  T + ++   VG+
Sbjct: 190 KRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGR 241



 Score = 78.2 bits (191), Expect = 6e-19
 Identities = 54/218 (24%), Positives = 105/218 (48%), Gaps = 6/218 (2%)

Query: 30  GRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPKSSQEAGIGIIHQE-- 87
           G ++   G  GAG++ + + + G    ++G ++  G + T   P  +   GIG + ++  
Sbjct: 281 GEILGFAGLMGAGRTEVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRK 340

Query: 88  -LNLIPQLTIAENIFLG--REFVNRFGKIDWKTMYAEADKLLAKLNLRFKS-DKLVGDLS 143
              L   +++  NI +   R+F++    +    +   A   +  L +R  S  + V  LS
Sbjct: 341 RFGLATGMSVESNIVMSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLS 400

Query: 144 IGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKSQGRGIVYISHRMKE 203
            G+QQ + IAK L  +  V+  DEPT  +       +++++R L  QG+ IV IS  + E
Sbjct: 401 GGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPE 460

Query: 204 IFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
           I  + D + V  +G+   E   A  T++ ++++   R+
Sbjct: 461 ILRMSDRIVVMCEGRITGELAAAGATQERIMQLATQRE 498


Lambda     K      H
   0.318    0.137    0.380 

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: 622
Number of extensions: 27
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 501
Length of database: 503
Length adjustment: 34
Effective length of query: 467
Effective length of database: 469
Effective search space:   219023
Effective search space used:   219023
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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