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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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:

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:

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:

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:

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