GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Klebsiella michiganensis M5al

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  502 bits (1293), Expect = e-146
 Identities = 251/492 (51%), Positives = 347/492 (70%), Gaps = 2/492 (0%)

Query: 12  YLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTIL 71
           + LE  GI+K FPGVKALDNV+L+VRP ++HALMGENGAGKSTL+KCL GIY+ D G I 
Sbjct: 4   FALEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIR 63

Query: 72  FQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETK 131
            +G+ + F    +AL +GISM+HQELNLV   +V +N+WLGR P K  FVD  ++ R+T+
Sbjct: 64  VKGEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQ 123

Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
            + D+L+I +     VG LS++  QM+EIAKA S+NA IVIMDEPTS+LTE EV HLFTI
Sbjct: 124 DLLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTI 183

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           IR L+++G  I+YISHKM+EIF + DE++V RDG W+ ++     T   +I  MVGR L 
Sbjct: 184 IRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGRELT 243

Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
           Q FP   N  GE +L VRNL+  R+ +  D++F + +GEILG+AGLVGA R++++E+LFG
Sbjct: 244 QLFPKFNNAIGEEVLTVRNLS--RKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFG 301

Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
           + +  +G + + G  +N  + + AI  G AL+TE+R+ +G++  L +  N  I  +  Y 
Sbjct: 302 MEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYI 361

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
            K G + + +M  D    I  + +KTP     I +LSGGNQQKV+I RWLL QP+IL+LD
Sbjct: 362 GKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILD 421

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EPTRGIDVGAK EIY LI+ELA +G  +I++SSE+PE+LG++DR++VM  G ++GI+D +
Sbjct: 422 EPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKE 481

Query: 492 TTTQNEILRLAS 503
              Q  IL LAS
Sbjct: 482 DADQETILSLAS 493


Lambda     K      H
   0.318    0.136    0.384 

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: 655
Number of extensions: 20
Number of successful extensions: 5
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: 506
Length of database: 494
Length adjustment: 34
Effective length of query: 472
Effective length of database: 460
Effective search space:   217120
Effective search space used:   217120
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