GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Burkholderia phytofirmans PsJN

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate BPHYT_RS16155 BPHYT_RS16155 carbohydrate kinase

Query= reanno::Smeli:SMc03164
         (484 letters)



>FitnessBrowser__BFirm:BPHYT_RS16155
          Length = 493

 Score =  229 bits (585), Expect = 1e-64
 Identities = 163/499 (32%), Positives = 238/499 (47%), Gaps = 37/499 (7%)

Query: 2   YLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLRE 61
           +LG+DLGT  +K  ++D   R    AS A  ++ P  GW+E     W RA  EA ARL +
Sbjct: 3   FLGIDLGTGSLKVAIVDENGREQAVASVAYPIETPQAGWAETSVQTWWRALCEAAARLPD 62

Query: 62  THAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDGDPQFRALTG 121
              +    VR IG SGQMHG  L+D     +RP +LW DTR+    A L+  P+ +    
Sbjct: 63  GLRRD---VRAIGFSGQMHGVVLIDAAGEAVRPAMLWPDTRAL---ALLEAWPEPQP--- 113

Query: 122 NIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDTG 181
           N V PG   P L W+  +EP+  +R RW L PKD+LR+ L G   ++ SD+  T+  D  
Sbjct: 114 NPVAPGMAGPLLRWIVLHEPQSASRTRWALQPKDWLRVALGGAVATDPSDACATALADPA 173

Query: 182 KRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASAC 241
              W A+LL    +       L     A G L    A   G+  G+V+A GA D   +A 
Sbjct: 174 G-VWDAALLDRLEIPHEWFAPLAPSYAAGGVLSESAARALGLRAGIVLATGAADTPCAAL 232

Query: 242 GMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDALN 301
           G G   +G A ++ GT G +    A + P     +H +  A  + W++M  + +   AL 
Sbjct: 233 GSGLAHDGDALLTTGTGGQIVVL-AEHAPAAVKGLHRY-RAASDHWYRMAAMQNVGIALE 290

Query: 302 ----WHS-------------GVTGRSAAELTSELGESLKAPGSVTFLPYLSGERTPHNDA 344
               W S                  +A   T+    +  A   +TFLPYL+GERTP  + 
Sbjct: 291 RARGWLSYEWADAYRDAFGDATNATNATNATATFSANTAAASGLTFLPYLTGERTPWLNP 350

Query: 345 TIRGVFAGLGHESSRAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWL 404
             RG + GL  + +R  + +A  EGV+F++R  L+A+RA+G  +  +   GGGS    W 
Sbjct: 351 MARGGWLGLALDHTRGTMMRAAFEGVAFSLRAGLDAIRASGATVTALKLAGGGSVDARWR 410

Query: 405 SSIATALNLPVDLPADGDFGAAFGAARLGLIAA---TGADPAAVCTAPETAETIAPEASL 461
             +A ALN+ +    D    A  GAA LG +A+      D AA+  AP       P+   
Sbjct: 411 QLLADALNVELH-AVDCPNAAPRGAAILGGLASGHWHARDLAAL--APGATRVAGPQGD- 466

Query: 462 VPAYEDAYQRYRRLYPAIK 480
             A  + Y+R+  LY  I+
Sbjct: 467 -AALAERYERFLDLYGRIE 484


Lambda     K      H
   0.317    0.132    0.401 

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: 672
Number of extensions: 34
Number of successful extensions: 4
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: 484
Length of database: 493
Length adjustment: 34
Effective length of query: 450
Effective length of database: 459
Effective search space:   206550
Effective search space used:   206550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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