Aligments for a candidate for HSERO_RS05250 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for HSERO_RS05250 in Burkholderia phytofirmans PsJN

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  505 bits (1300), Expect = e-147
 Identities = 271/496 (54%), Positives = 347/496 (69%), Gaps = 2/496 (0%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           ++ L+ V KRFPGV+ALD    +L AGEVHA+ GENGAGKSTLMKI+SG Y+ D G +  
Sbjct: 23  ILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRY 82

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            G PV+ +    AQA GI IIHQELNL+ HLS A+NI++ REP++  G F+D   LN  A
Sbjct: 83  RGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKR--GPFVDYRTLNSNA 140

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
                R+ L++ PST VG L++A+QQMVEIAKALS D+RVLIMDEPT++L  +E  +LFR
Sbjct: 141 QRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFR 200

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
           IIR+L+A GV I+YISH++DE+ +I DRV+V+RDG++IAT     T+++ I++ MVGR L
Sbjct: 201 IIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRPL 260

Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321
           D        T  N ++L VR L R      +SF LRKGEILGFAGLMGAGRTE ARAIFG
Sbjct: 261 DDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAIFG 320

Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT 381
           A+  ++G I +      I SP +A+ HGI YLSEDRK  GLA+ M V ANI L+++   +
Sbjct: 321 AERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAIS 380

Query: 382 RVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDE 441
             GF+        A+ YVR+L I+TP+V+Q AR LSGGNQQKIVI+KWL R   ILFFDE
Sbjct: 381 SRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDE 440

Query: 442 PTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARAD 501
           PTRGIDVGAK  IY L+D LA  G  +V+ISSELPE+L M+ R+ V  EGRIT  L    
Sbjct: 441 PTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETRQ 500

Query: 502 ATQEKIMQLATQRESA 517
            +QE+I+  A+ R  A
Sbjct: 501 TSQEEILHHASGRSHA 516


Lambda     K      H
   0.320    0.135    0.372 

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: 672
Number of extensions: 20
Number of successful extensions: 6
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: 520
Length of database: 516
Length adjustment: 35
Effective length of query: 485
Effective length of database: 481
Effective search space:   233285
Effective search space used:   233285
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.

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, or view the source code.

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