GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Klebsiella michiganensis M5al

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  396 bits (1018), Expect = e-115
 Identities = 217/497 (43%), Positives = 323/497 (64%), Gaps = 14/497 (2%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           LE   I+K FPGVKAL+NV+L+V+ G +HAL+GENGAGKSTLMK L G+Y     +G I 
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPD--KGAIR 63

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125
            +G    F+   D+   GI +IHQEL LVP +++AENI+LG E    G +  +Q   +T+
Sbjct: 64  VKGEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQ 123

Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185
           +LL K+ ++ S + L+ ++ +  QQ+VEIAKA+S +  ++I+DEPT++L ES+   L  +
Sbjct: 124 DLLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTI 183

Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGRD 245
           + + R QG   I I+HK++E+  + D+I+V RDG  V +      E +   +I  MVGR+
Sbjct: 184 IRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQT--TEFTRQSLITQMVGRE 241

Query: 246 LEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTE 305
           L   +P  +  IGE +L V+N +        +   HDIN +VR+GE++G+AGL+GAGR+E
Sbjct: 242 LTQLFPKFNNAIGEEVLTVRNLSR-------KGAFHDINFSVRRGEILGVAGLVGAGRSE 294

Query: 306 FAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNT 365
              S+FG       +G+VLIDG PV++ +   AI+ G+A +TEDRK  GL L  ++L N 
Sbjct: 295 VMESLFGMEKAD--SGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENM 352

Query: 366 TLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424
           ++  +   + K   +  +K  +   +   RL I++  + Q   NLSGGNQQKV++++WL 
Sbjct: 353 SIVKMPEYIGKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLL 412

Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484
           + P +LILDEPTRGIDVGAK EIY +I++LA  G  V+M+SSE+PE+LG  DR+ VM+EG
Sbjct: 413 AQPKILILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEG 472

Query: 485 RIVAELPKGEASQESIM 501
           RI   L K +A QE+I+
Sbjct: 473 RITGILDKEDADQETIL 489


Lambda     K      H
   0.316    0.135    0.374 

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: 667
Number of extensions: 38
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 494
Length adjustment: 34
Effective length of query: 478
Effective length of database: 460
Effective search space:   219880
Effective search space used:   219880
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 (21.6 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