Aligments for a candidate for xylK_Tm in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for xylK_Tm in Burkholderia phytofirmans PsJN

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS16060 BPHYT_RS16060 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:Q9WXX0
         (520 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS16060 BPHYT_RS16060
           ribonucleotide-diphosphate reductase subunit alpha
          Length = 506

 Score =  393 bits (1010), Expect = e-114
 Identities = 208/499 (41%), Positives = 309/499 (61%), Gaps = 9/499 (1%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           ILK   I K FPGV A+  +  E+   EI +L+GENGAGKSTL+KIL G+ +PD G I +
Sbjct: 4   ILKLDNITKSFPGVKALQGIHLEIERGEIHALLGENGAGKSTLMKILCGIYQPDEGTITI 63

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            GE   F +  DA   G+ ++ QE +L   +   EN+FL  E   G        ++   M
Sbjct: 64  EGEARHFSNYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGRELKNGL-----GLLERGKM 118

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
              +  +   +G        +R L+ AQ+Q VEI KAL  E RI+ +DEPT++LT  E E
Sbjct: 119 RRAAAAIFQRLGVTIDLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEAE 178

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            LF I+  LK +G++++F+SH L+E+  + DRI V+RDG+ +G  +  + +V  +++MMV
Sbjct: 179 HLFAIMRELKQQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSNVGHLVEMMV 238

Query: 254 GREVE--FFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311
           GR +E  F P        +I L+V  L+       +SF +R+GE+LGFAGLVG+GRTET 
Sbjct: 239 GRRIENSFPPKPPLRADAKIVLDVEKLQLLKDSPVLSFTLREGEILGFAGLVGSGRTETA 298

Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371
           L V G +     +I +NG   ++ +P DA++ G+G++PE RK +GL+   ++K NI + +
Sbjct: 299 LAVIGADPAYVKEIRINGTAAKLSDPADALRAGVGILPESRKTEGLITDFSIKQNISINN 358

Query: 372 LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431
           L K       +D+R E   + D +KR+ +K P+++     LSGGNQQKVV+A+WL  + +
Sbjct: 359 LGKYRSLRFFIDQRSEARATADIMKRVGVKAPTMHTEVATLSGGNQQKVVIARWLNHHTN 418

Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491
           ILIFDEPTRGIDVGAKAEI+ ++REL A+G ++IMISSELPEI+ + DR+ V  +G I A
Sbjct: 419 ILIFDEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSELPEIVGMCDRVAVFRQGRIEA 478

Query: 492 VLDNREKRVTQEEIMYYAS 510
           +L+     +    +M YA+
Sbjct: 479 MLEG--DAIDSNAVMTYAT 495


Lambda     K      H
   0.319    0.138    0.381 

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: 635
Number of extensions: 27
Number of successful extensions: 7
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: 506
Length adjustment: 35
Effective length of query: 485
Effective length of database: 471
Effective search space:   228435
Effective search space used:   228435
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 (21.7 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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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, 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