GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Escherichia coli BW25113

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  410 bits (1054), Expect = e-119
 Identities = 222/500 (44%), Positives = 325/500 (65%), Gaps = 10/500 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L+ KGI K FPGV A+      VY   +++L+GENGAGKST++K+LTG+   DAG +L 
Sbjct: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G+   F  P  + + GI +IHQELNL   +T+AENIFL  E V         ++D   M
Sbjct: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNR-----FGKIDWKTM 118

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
           Y  + +LL  +  +F  D LV +L+   +QMVEI K L  E ++I MDEPT +LT  ETE
Sbjct: 119 YAEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETE 178

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            LF +I  LKS+G  +V++SHR+ E+  I D + V RDG+ I E +      D++I+MMV
Sbjct: 179 SLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMV 238

Query: 254 GREVEF-FPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312
           GR++E  +PH ++  PG+I L+V NL     V +VSF +RKGE+LG +GL+GAGRTE M 
Sbjct: 239 GRKLEDQYPH-LDKAPGDIRLKVDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGRTELMK 296

Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372
           +++G   + SG + ++G +V  ++P+D +  GI  I EDRK  GLVL M+VK+N+ L +L
Sbjct: 297 VLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTAL 356

Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432
           +  SR G  L    E++   D+++  ++KTPS+ Q    LSGGNQQKV +A+ L T   +
Sbjct: 357 RYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKV 416

Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492
           LI DEPTRG+DVGAK EI+++I +  A G ++I++SSE+PE+L +SDRI+VM EG ++  
Sbjct: 417 LILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSG- 475

Query: 493 LDNREKRVTQEEIMYYASGQ 512
            +   ++ TQE +M  A G+
Sbjct: 476 -EFTREQATQEVLMAAAVGK 494


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: 683
Number of extensions: 32
Number of successful extensions: 6
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: 501
Length adjustment: 34
Effective length of query: 486
Effective length of database: 467
Effective search space:   226962
Effective search space used:   226962
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