GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pantoea rwandensis LMG 26275

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>NCBI__GCF_002095475.1:WP_084935209.1
          Length = 494

 Score =  417 bits (1073), Expect = e-121
 Identities = 230/498 (46%), Positives = 327/498 (65%), Gaps = 12/498 (2%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L+A+GI K FPGV A+DNV   +    + +L+GENGAGKSTL+K L G+ +PD G I + 
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIK 65

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
           GE V+F   +DA + GIS+IHQELNL   MTVAENI+L  E ++         VD   + 
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPMK------YGFVDHGKLN 119

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
            +++ELL+ +  +   D +V  L+ A +QMVEI KA+     I+ MDEPTS+LT  E   
Sbjct: 120 KQTQELLNRLNIRLKADRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAH 179

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254
           LF II  L+ +G +++++SH++DE+  I+D I + RDG  +G     EF   ++I  MVG
Sbjct: 180 LFTIIRDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVG 239

Query: 255 REV-EFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313
           RE+ + FP       G   L VRNL  KD+  +++F VRKGE+LG AGLVGAGR+E M  
Sbjct: 240 RELTQLFPK-FNGEIGADVLTVRNLTCKDRFTDINFTVRKGEILGVAGLVGAGRSEVMES 298

Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373
           +FG+   +SG++ ++G  V+I +P  AI+ G+  + EDRK  GL L ++V +N+ + ++ 
Sbjct: 299 LFGMESFDSGEVLIDGVPVKIDSPSTAIEKGMAFLTEDRKKSGLFLVLSVMENMSIVNMP 358

Query: 374 K-ISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432
             +S+ G V   +  ++  E  +++L+IKTP++ QI  NLSGGNQQKV++A+WL     I
Sbjct: 359 DYVSKAGFVSHMKMAQDCMEQ-IRKLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKI 417

Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492
           LI DEPTRGIDVGAKAEI+R+I ELA +G A+IM+SSELPEIL +SDR++VM  G IT +
Sbjct: 418 LILDEPTRGIDVGAKAEIYRLISELANRGVAIIMVSSELPEILGMSDRVMVMHGGRITGI 477

Query: 493 LDNREKRVTQEEIMYYAS 510
           LD  E    QE I+  AS
Sbjct: 478 LDKEE--ANQETILSLAS 493


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: 699
Number of extensions: 39
Number of successful extensions: 8
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: 494
Length adjustment: 34
Effective length of query: 486
Effective length of database: 460
Effective search space:   223560
Effective search space used:   223560
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 24 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