Alignments for a candidate for HSERO_RS03640 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Burkholderia phytofirmans PsJN

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__BFirm:BPHYT_RS20740
          Length = 503

 Score =  412 bits (1059), Expect = e-119
 Identities = 227/497 (45%), Positives = 320/497 (64%), Gaps = 5/497 (1%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           TPL+ ++ + K F    AL ++   +  GE+HALMGENGAGKSTLMK+L+GV+  D GEI
Sbjct: 2   TPLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEI 61

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL-IDHAAMRS 122
           L +G+PV  + P  ++A G+ +I+QEL +  ++++A N+F+G E R RLGL +D   + +
Sbjct: 62  LYEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNA 121

Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182
           +   +L ++        L   L++A QQ VEIA+AL   SR++IMDEPT+AL++ E  +L
Sbjct: 122 QAHDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181

Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242
           F ++R L+  G+ IIYISH+M E+  +ADRVTVLRDG +V  +   +   + I+ MMVGR
Sbjct: 182 FRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGR 241

Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELA 302
           +L++    Q IA      L      R  AG  +R  SF +R GE+LGFAGL+GAGRTE+A
Sbjct: 242 TLTDAAPSQHIANQGEVALEVT---RLNAGPLVRDVSFALRKGEILGFAGLMGAGRTEVA 298

Query: 303 RLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362
           R +FGADP   G+I+++G    I  P  A+  GI Y+ EDRK  GL   M+V +N  M+ 
Sbjct: 299 RAVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSN 358

Query: 363 ASRHTRLGL-VRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPK 421
             +   L   +R   +   A   I  L ++       V  LSGGNQQK+++A+WLE    
Sbjct: 359 LRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCD 418

Query: 422 VLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITG 481
           VL  DEPTRG+D+ AKSEIY+L+  LA QG A+V+ISSELPE++ + DR++VM EG ITG
Sbjct: 419 VLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITG 478

Query: 482 ELAGAAITQENIMRLAT 498
           ELA A  TQE IM+LAT
Sbjct: 479 ELAAAGATQERIMQLAT 495



 Score =  106 bits (264), Expect = 2e-27
 Identities = 71/237 (29%), Positives = 119/237 (50%), Gaps = 6/237 (2%)

Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA 334
           +    F++ AGEV    G  GAG++ L ++L G   R  G+IL EG+PV    PR A   
Sbjct: 20  LHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILYEGQPVDFQSPREAQAV 79

Query: 335 GIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRS-LGGVARAAIQRLNVKVA 393
           G+  + ++ +   L   + +A N  +    R  RLGL      L   A   + R++V + 
Sbjct: 80  GVGIIHQELQ---LMNHLTIAQNMFIGREPRG-RLGLFLDEDKLNAQAHDILARMHVTL- 134

Query: 394 HPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVA 453
            P   V  L+   QQ V +A+ L    +VLI+DEPT  ++    +E+++++  L  +GV 
Sbjct: 135 DPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFRIIRDLKKRGVG 194

Query: 454 VVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASH 510
           ++ IS ++ E+  I DRV V+R+G     +A    T + I+ +     +   AP+ H
Sbjct: 195 IIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGRTLTDAAPSQH 251



 Score = 93.6 bits (231), Expect = 2e-23
 Identities = 64/226 (28%), Positives = 111/226 (49%), Gaps = 8/226 (3%)

Query: 24  DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83
           D+   +R GEI    G  GAG++ + + + G    + GEI++ G    +R+P  + A GI
Sbjct: 273 DVSFALRKGEILGFAGLMGAGRTEVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGI 332

Query: 84  NLIYQE---LAVAPNISVAANVFMGSELRTRLGL---IDHAAMRSRTDAVLRQLGAGFGA 137
             + ++     +A  +SV +N+ M S LR  L L   +    +R      +  L     +
Sbjct: 333 GYLSEDRKRFGLATGMSVESNIVM-SNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPS 391

Query: 138 SDLAGRL-SIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAI 196
           +    RL S   QQ++ IA+ L     ++  DEPT  +      +++ ++R L D+G AI
Sbjct: 392 ATQEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAI 451

Query: 197 IYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242
           + IS  + E+  ++DR+ V+ +G   GEL       ERI+Q+   R
Sbjct: 452 VMISSELPEILRMSDRIVVMCEGRITGELAAAGATQERIMQLATQR 497


Lambda     K      H
   0.320    0.135    0.378 

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: 683
Number of extensions: 21
Number of successful extensions: 8
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: 521
Length of database: 503
Length adjustment: 35
Effective length of query: 486
Effective length of database: 468
Effective search space:   227448
Effective search space used:   227448
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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