Alignments for a candidate for xylK_Tm in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Paraburkholderia bryophila 376MFSha3.1

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Burk376:H281DRAFT_02712
          Length = 505

 Score =  402 bits (1033), Expect = e-116
 Identities = 224/504 (44%), Positives = 322/504 (63%), Gaps = 17/504 (3%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPD-AGEILV 73
           L+ + I + FPGV A+D V+ E+   E+++L GENGAGKSTL+KILTG+  PD  G ILV
Sbjct: 10  LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G+ V       A   G+++I+QEL +  N+TV ENIFLA E      RT    +D   M
Sbjct: 70  EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREP-----RTRLGLIDRPRM 124

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
           Y  ++E+L  I     P   V  L+  Q+QM+EI KAL    + I MDEPT+SL+  ET 
Sbjct: 125 YREAREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETS 184

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            L  I++ L+ R I+VV++SHRL+E+  ++DR+ V+RDG+ +G     +   +T++++MV
Sbjct: 185 VLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMV 244

Query: 254 GREV-EFFPHGIETRPGEIALEVRNLKWKD------KVKNVSFEVRKGEVLGFAGLVGAG 306
            RE+ E +         +  LEVR L  K       +++++SF + +GEVLG AGLVG+G
Sbjct: 245 ARELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSG 304

Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366
           RTE M ++FG+    +G + + G+ V I+NP DAI+ GIG + EDRK QGL+L MTV++N
Sbjct: 305 RTEIMEMIFGMRAC-TGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVREN 363

Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426
             L  L++ S +  V   R E E    +V+ L IKTP + Q   NLSGGNQQK+V+AKW+
Sbjct: 364 FSLTHLERYSPFQFVQHAR-ERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWV 422

Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWE 486
           A +  +LI DEPTRGIDVGAKAE+H +I  LAA+G  VI+ISS+L E+L +SDRI+ + E
Sbjct: 423 ARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVRE 482

Query: 487 GEITAVLDNREKRVTQEEIMYYAS 510
           G I+  L   +   +QE++M  A+
Sbjct: 483 GRISGELSRAQ--ASQEKVMALAT 504


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: 659
Number of extensions: 31
Number of successful extensions: 9
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: 505
Length adjustment: 35
Effective length of query: 485
Effective length of database: 470
Effective search space:   227950
Effective search space used:   227950
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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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