Alignments for a candidate for BPHYT_RS34245 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Burkholderia phytofirmans PsJN

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

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__BFirm:BPHYT_RS28215
          Length = 509

 Score =  321 bits (823), Expect = 3e-92
 Identities = 193/498 (38%), Positives = 280/498 (56%), Gaps = 8/498 (1%)

Query: 5   MSELTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64
           M + TS+VP +E    +K FG   AL+D  + + PGE HAL+G NGAGKST+V IL G+ 
Sbjct: 1   MQQPTSAVPRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVH 60

Query: 65  KPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGVID 123
           +PDTGE+   G A       +A    +A +YQ  T+  DLS+AEN+F+ RQP+ R G I 
Sbjct: 61  QPDTGELVVDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQ 120

Query: 124 WQAMRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDG 183
           + AMRR+   LL    +D+R D     LS+  +Q++EIA+ALS  A  +I+DEPTA L  
Sbjct: 121 YDAMRREVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSL 180

Query: 184 DEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243
            E++RLF  + +L+   V  LFI+H L EV+ + Q VT++RD   +     + L  E ++
Sbjct: 181 PEVERLFTIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIV 240

Query: 244 EAMTGERGGLAVADAAARGALPADTAVALELKELTGAD-YEGVSFTVKRGEVVGLTGATS 302
             M G        +     A      V L ++ LT    ++ +SF V+ GE+V L G   
Sbjct: 241 AKMVGRD-----LETFYPKAERPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVG 295

Query: 303 SGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVA 362
           +GR+ VA AI G+     G I + G  L  G   A++  G+  VP+DR  +GL L  S+A
Sbjct: 296 AGRSEVARAIFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIA 355

Query: 363 ENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARA 422
            NASMT+   L K G+ +   +     +    L + A  P   V  LSGGNQQKVV+ + 
Sbjct: 356 RNASMTVLGRLVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKW 415

Query: 423 LATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMF 481
           LAT P VL++ +PT G+DV +K  + S +  +  +G AVL++S EL + L   DRVLVM 
Sbjct: 416 LATGPKVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMH 475

Query: 482 RGRVAAEFPAGWQDHDLI 499
            GR++A+      D + I
Sbjct: 476 EGRISADIARADADEERI 493



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 14/228 (6%)

Query: 32  DVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRERV 91
           D+S  V  GE  AL G  GAG+S +   + G+   D+GE+  +G    +     A R  +
Sbjct: 277 DISFDVRAGEIVALAGLVGAGRSEVARAIFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGL 336

Query: 92  ACVYQ---HSTIIRDLSVAEN--LFINRQPLRGGVIDWQAMRRDARALLDHWKIDVR--- 143
           A V +      +  +LS+A N  + +  + ++ G+I      R    L + W   +R   
Sbjct: 337 ALVPEDRRQQGLALELSIARNASMTVLGRLVKHGLIS----ARSETQLANQWGTRLRLKA 392

Query: 144 --EDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGV 201
              +A  G LS   +Q V + + L+ G + +I+DEPT  +D      ++  ++EL R+G+
Sbjct: 393 GDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDEPTRGIDVGAKAEVYSALAELVRDGM 452

Query: 202 TFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGE 249
             L IS  L EV  +   V V+ + R       +    E+++ A  G+
Sbjct: 453 AVLMISSELPEVLGMADRVLVMHEGRISADIARADADEERIMGAALGQ 500


Lambda     K      H
   0.318    0.134    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: 648
Number of extensions: 25
Number of successful extensions: 8
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: 510
Length of database: 509
Length adjustment: 34
Effective length of query: 476
Effective length of database: 475
Effective search space:   226100
Effective search space used:   226100
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.

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Protein sequences (fasta format)
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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