Alignments for a candidate for xylG in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Klebsiella michiganensis M5al

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  450 bits (1157), Expect = e-131
 Identities = 230/489 (47%), Positives = 346/489 (70%), Gaps = 3/489 (0%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           LE + I K FPGV AL  VS+   PG VHA++GENGAGKSTLMK + G+Y+PD+G I  +
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124
           G  V++    +A+ +GI  + QEL+++ +++VAENI++G E  +  F+D++++ R+ +  
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDL 125

Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184
           + ++  I +  +  +G+ SIA QQMVEIA+AV   A ++I+DEPTS+LT+ E   LF ++
Sbjct: 126 L-DKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTII 184

Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244
           + L+++G AII+ISH+++EIF I D++SV RDG ++G+      T++ ++  MVGR+L +
Sbjct: 185 RDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGRELTQ 244

Query: 245 FYIKEAHEPGEVVLEVKNLSGE-RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRP 303
            + K  +  GE VL V+NLS +  F +++FS+RRGEILG AGLVGAGR+E+ME++FG   
Sbjct: 245 LFPKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEK 304

Query: 304 KRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL-DRIKKG 362
              GE+ I+G  V I+ P  AIE+G+ L+ EDRKK GL L++S++ N+S+  + + I K 
Sbjct: 305 ADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKT 364

Query: 363 PFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPT 422
            F+   +  E     I+  +I+    D+ +  LSGGNQQKV++A+WL  +PKILILDEPT
Sbjct: 365 GFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPT 424

Query: 423 RGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEAS 482
           RGIDVGAKAEIY ++S+LA  GV VIM+SSELPE+L MSDR+ VM  G++ GI+D ++A 
Sbjct: 425 RGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKEDAD 484

Query: 483 QEKVMKLAA 491
           QE ++ LA+
Sbjct: 485 QETILSLAS 493



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 64/227 (28%), Positives = 119/227 (52%), Gaps = 8/227 (3%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFG-FRPKRGGEIYIEGKRVEINHPLDAIEQ 327
           +NVS  +R G +    G  GAG++ LM+ + G +RP +G  I ++G+ V+    +DA+  
Sbjct: 22  DNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGA-IRVKGEPVQFQDTMDALRS 80

Query: 328 GIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAY 387
           GI ++ ++   L L+  M++  N+ L   + +K G F+  ++        +   +IR + 
Sbjct: 81  GISMIHQE---LNLVPHMTVAENIWL-GREPMKYG-FVDHRQLARQTQDLLDKLNIRLS- 134

Query: 388 PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGV 447
            DR V  LS  +QQ V +AK ++    I+I+DEPT  +     A ++ I+  L ++G  +
Sbjct: 135 ADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDLRQQGKAI 194

Query: 448 IMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           I IS ++ E+  ++D I+V   G   G     E +++ ++    G E
Sbjct: 195 IYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGRE 241


Lambda     K      H
   0.318    0.138    0.385 

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: 645
Number of extensions: 29
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 494
Length of database: 494
Length adjustment: 34
Effective length of query: 460
Effective length of database: 460
Effective search space:   211600
Effective search space used:   211600
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources