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_RS06145 BWI76_RS06145 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Koxy:BWI76_RS06145
          Length = 428

 Score =  580 bits (1496), Expect = e-170
 Identities = 276/418 (66%), Positives = 334/418 (79%)

Query: 5   RLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFF 64
           +L  RRWWY+MPI+FITYSLAYLDRANYGFAAA+G+  DL IT   +SL+GALFFLGYFF
Sbjct: 6   KLPARRWWYLMPIIFITYSLAYLDRANYGFAAAAGIESDLGITKGTASLIGALFFLGYFF 65

Query: 65  FQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAML 124
           FQVPGAIYA KRSV+K+IF SLILWG  A  TG V ++ +L+AIRF LGVVEAAVMPAML
Sbjct: 66  FQVPGAIYAVKRSVRKMIFCSLILWGFCAAATGFVSNIPMLMAIRFTLGVVEAAVMPAML 125

Query: 125 IYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFI 184
           IY+ +WFT+ ERSRANTFLILGNPVT+LWMS+VSGYL++ + WR MFIIEG+PAVLWA  
Sbjct: 126 IYISNWFTKTERSRANTFLILGNPVTVLWMSIVSGYLIQAWGWREMFIIEGIPAVLWAVC 185

Query: 185 WWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWS 244
           WW LV D+P + SWL  QEK  L++ + +EQ  IKPV+NY EA RS  VI+L   +  WS
Sbjct: 186 WWILVRDKPSEVSWLNEQEKETLQKVMDSEQSHIKPVRNYGEALRSRNVIMLCAVHALWS 245

Query: 245 IGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPP 304
           IGVYGF++W+PSILK AA +DIV  GWL+AVPYL A++ ML VSW SD+ Q RK F+WP 
Sbjct: 246 IGVYGFMMWMPSILKNAAQMDIVAVGWLAAVPYLAAIILMLTVSWLSDKFQNRKLFIWPL 305

Query: 305 LLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALI 364
           LLIAA+AF+GS+++G + FW SY LLVIA ACMYAPYGPFFA++PELLP NV+G +M LI
Sbjct: 306 LLIAAIAFFGSWMVGNQAFWLSYALLVIAAACMYAPYGPFFALIPELLPRNVSGVSMGLI 365

Query: 365 NSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQARRQQLA 422
           NS GALG+F G+WLVGYLNG+TGGPG SY FM  ALL +V L   +  + Q+    +A
Sbjct: 366 NSFGALGAFLGAWLVGYLNGITGGPGVSYTFMAVALLSSVVLMFNVRANPQSSSPAVA 423


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: 798
Number of extensions: 35
Number of successful extensions: 2
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: 428
Length adjustment: 32
Effective length of query: 393
Effective length of database: 396
Effective search space:   155628
Effective search space used:   155628
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