Alignments for a candidate for araVsh in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Burkholderia phytofirmans PsJN

Align ABC transporter related (characterized, see rationale)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__BFirm:BPHYT_RS28215
          Length = 509

 Score =  360 bits (924), Expect = e-104
 Identities = 193/492 (39%), Positives = 312/492 (63%), Gaps = 7/492 (1%)

Query: 5   LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64
           LEL+  SK +  V+AL D  L L+ GEVHALLGENGAGKST+VK++ G    D G+++  
Sbjct: 11  LELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELVVD 70

Query: 65  GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEP-RRLGLIHFKKMYADARA 123
           GE + F TP +A+ AG++ +YQE  L  +L++A+N+F+G +P  R+G I +  M  +   
Sbjct: 71  GEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREVDG 130

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +L    +D+     +   SIA QQ+I IA+ ++++A VL++DEPTA+L   EV+ LF I+
Sbjct: 131 LLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFTIV 190

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
            +L+ + VAI+FITH LD+V+ ++ R+T++R+G  + + LT +L    ++  M+GR L E
Sbjct: 191 RKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRDL-E 249

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
               K E+     R     LS+  ++  G  + ++  V  G+ V LAGL+G+GRSEV  A
Sbjct: 250 TFYPKAERPPGEVR-----LSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARA 304

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363
           +FG+D +DSG I +AG++L   +P  A+ AG+AL PEDR+  G+   LSI  N  + +  
Sbjct: 305 IFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLG 364

Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423
           R+     +S   + ++A  +  +L++   D + P+  LSGGNQQKV+L +WLA  P +L+
Sbjct: 365 RLVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLI 424

Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483
           +DEPTRGID+GA AE+   +  L  +GM++L+ SSEL E++  +++V+V+ +     +++
Sbjct: 425 IDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADIA 484

Query: 484 GAELTSQHVMQA 495
            A+   + +M A
Sbjct: 485 RADADEERIMGA 496



 Score = 91.3 bits (225), Expect = 7e-23
 Identities = 64/231 (27%), Positives = 117/231 (50%), Gaps = 6/231 (2%)

Query: 17  VKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDA 76
           V   +D+S  + AGE+ AL G  GAG+S + + + G    D G+I   G+      P  A
Sbjct: 272 VGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGIDPLDSGEIWIAGKRLTAGRPAAA 331

Query: 77  QKAGISTVYQE---VNLVPNLTVAQNLFLGYEPRRL--GLIHFKKMYADARAVLTQFKLD 131
            +AG++ V ++     L   L++A+N  +    R +  GLI  +     A    T+ +L 
Sbjct: 332 VRAGLALVPEDRRQQGLALELSIARNASMTVLGRLVKHGLISARSETQLANQWGTRLRLK 391

Query: 132 I-DVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190
             D +AP+   S   QQ + + + +A   KVL++DEPT  +D      ++  L +L   G
Sbjct: 392 AGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDEPTRGIDVGAKAEVYSALAELVRDG 451

Query: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241
           +A++ I+  L +V  ++DR+ V+  G+   +   A+  + +++ A LG+ +
Sbjct: 452 MAVLMISSELPEVLGMADRVLVMHEGRISADIARADADEERIMGAALGQPM 502


Lambda     K      H
   0.319    0.136    0.377 

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: 625
Number of extensions: 32
Number of successful extensions: 7
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: 499
Length of database: 509
Length adjustment: 34
Effective length of query: 465
Effective length of database: 475
Effective search space:   220875
Effective search space used:   220875
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 (21.8 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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