GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Klebsiella michiganensis M5al

Align KguT (characterized, see rationale)
to candidate BWI76_RS27095 BWI76_RS27095 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Koxy:BWI76_RS27095
          Length = 439

 Score =  273 bits (699), Expect = 6e-78
 Identities = 161/412 (39%), Positives = 238/412 (57%), Gaps = 11/412 (2%)

Query: 9   RRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVP 68
           +RW  I+P + IT  ++Y+DR N  FA   GM  DL I+  ++ L G +FF+GY F QVP
Sbjct: 15  QRWLRIIPPILITCIISYMDRVNIAFAMPGGMDADLGISATMAGLAGGIFFIGYLFLQVP 74

Query: 69  GAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLC 128
           G   A   S KK I  SL+ W  ++ LTG++ +   L+A+RFLLGV E  ++P +L  + 
Sbjct: 75  GGKIAVHGSGKKFIGWSLVAWAVISVLTGLITNQYQLLALRFLLGVAEGGMLPVVLTMIS 134

Query: 129 HWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIWWRL 188
           +WF  AER RAN  +I+  P+  +  + +SG+++   DWRW+FIIEGL +++   +W   
Sbjct: 135 NWFPDAERGRANAIVIMFVPIAGIITAPLSGWIITVLDWRWLFIIEGLLSLVVLVLWAYT 194

Query: 189 VDDRPEQASWLKAQEKTALREALAAEQQGI--KPVKNYR-EAFRSPKVI--ILSLQYFCW 243
           + DRP++A W+   EK  L E LAAEQ+ I    VKN    A  S K +  +++L +F +
Sbjct: 195 IYDRPQEARWISEAEKRYLVETLAAEQKAIAGTEVKNASLSAVLSDKTMWQLIALNFF-Y 253

Query: 244 SIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWP 303
             G+YG+ LWLP+ILK+     +   G L+ +PY+GA+  M   S  SDR  KRK FV  
Sbjct: 254 QTGIYGYTLWLPTILKELTHSSMGQVGMLAILPYVGAIAGMFLFSSLSDRTGKRKLFVCL 313

Query: 304 PLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMAL 363
           PL+  AL  + S  L  +  W SY  LV  G  + +  G F+ I   L  + +AGGA  +
Sbjct: 314 PLIGFALCMFLSVALKNQ-IWLSYAALVGCGFFLQSAAGVFWTIPARLFSAEMAGGARGV 372

Query: 364 INSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAV-ALTAVLNPSQ 414
           IN++G LG F G + VG L  +       Y   C A+ +A+ AL A+L P++
Sbjct: 373 INALGNLGGFCGPYAVGVLITLYSKDAGVY---CLAISLALAALMALLLPAK 421


Lambda     K      H
   0.328    0.140    0.457 

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: 595
Number of extensions: 25
Number of successful extensions: 3
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: 425
Length of database: 439
Length adjustment: 32
Effective length of query: 393
Effective length of database: 407
Effective search space:   159951
Effective search space used:   159951
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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