Alignments for a candidate for HSERO_RS05250 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments 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_RS16930 BPHYT_RS16930 arabinose ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__BFirm:BPHYT_RS16930
          Length = 512

 Score =  404 bits (1037), Expect = e-117
 Identities = 218/498 (43%), Positives = 324/498 (65%), Gaps = 16/498 (3%)

Query: 27  NVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPV 86
           N+ K FPGV ALD   F++  G+VH LMGENGAGKSTL+KIL G YQ DSG +++DG  V
Sbjct: 9   NIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEV 68

Query: 87  EITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFA 146
             T    + A GI +IHQEL  +  L+ A+N+ +G+ P  ++G       +N++ A  F 
Sbjct: 69  RFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP-NSLGW------VNKREAKRFV 121

Query: 147 RMRLD-----MDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
           R RL+     +DP+  + +L++A++QMVEI KAL  ++RV+ +DEPT++L++ E   LF+
Sbjct: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVP-MQETSMDTIISMMVGRA 260
           ++RDL+A    ++YISH+MDE+ ++ D  ++ RDG+ IA+ P ++  + DTI+S MVGR 
Sbjct: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241

Query: 261 LDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320
           +             +V    +G+      +  SF +R+GEI+GF GL+GAGR+E+   ++
Sbjct: 242 ISDIYNYSA-RPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300

Query: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380
           GAD  + GE+++ G    ++S  +A+ HGI    EDRK  G+     V  NI +S    +
Sbjct: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360

Query: 381 TRVG-FMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLR-DCDILF 438
            RVG F+D++   E A  +++ L IKTPS  Q+ R LSGGNQQK ++++WL   D  ++ 
Sbjct: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 420

Query: 439 FDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELA 498
            DEPTRGIDVGAK EIY ++  LAE+G AIVMISSELPEVL +S R++VM +GRI+GEL 
Sbjct: 421 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT 480

Query: 499 RADATQEKIMQLATQRES 516
           R DAT++ ++ LA  + S
Sbjct: 481 RKDATEQSVLSLALPQSS 498



 Score = 93.6 bits (231), Expect = 2e-23
 Identities = 70/258 (27%), Positives = 130/258 (50%), Gaps = 11/258 (4%)

Query: 18  SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77
           S+ P+  +R   K   G        FE+  GE+    G  GAG+S LM ++ G   +  G
Sbjct: 249 SARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGG 308

Query: 78  DILLDGKPVEITEPRQAQALGIGII---HQELNLMNHLSAAQNIFIG-REPRKAMGLFID 133
           ++LLDGKP+++    +A   GI +     +E  ++   + ++NI I  R     +G+F+D
Sbjct: 309 ELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLD 368

Query: 134 EDELNRQAAAIFARMRLDMDPS--TPVGELTVARQQMVEIAKALSF-DSRVLIMDEPTAA 190
             +   + A  F ++     PS    +  L+   QQ   +++ L+  D +V+I+DEPT  
Sbjct: 369 RKK-EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRG 427

Query: 191 LNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMD 250
           ++     E++ +I  L  +G  IV IS ++ E+  ++DR+ VMR G+    +  ++ +  
Sbjct: 428 IDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQ 487

Query: 251 TIISMMV---GRALDGEQ 265
           +++S+ +     AL G Q
Sbjct: 488 SVLSLALPQSSTALPGTQ 505


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: 654
Number of extensions: 26
Number of successful extensions: 10
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 (21.8 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