GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Klebsiella michiganensis M5al

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__Koxy:BWI76_RS22920
          Length = 436

 Score =  266 bits (681), Expect = 7e-76
 Identities = 154/412 (37%), Positives = 234/412 (56%), Gaps = 6/412 (1%)

Query: 25  YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84
           Y +   +L S+FF+W     LNDIL+P  +  F L   +A L+Q  F+  YF++ +PAG+
Sbjct: 22  YIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFVIPIPAGI 81

Query: 85  LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144
           L+ +L YK GI+ GL +   GAA FWPAA +  Y  FL  LF++A G+  L+ AAN +V 
Sbjct: 82  LMKKLSYKAGIITGLFLYAFGAALFWPAAEVMNYTLFLIGLFIIAAGLGCLETAANPFVT 141

Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIA-KLSPAEQVAYRVQ 203
           +LGPE     RL LAQ  NS G  +A  FG  LILS     ++ +  K++P +  AY+  
Sbjct: 142 VLGPESGGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMAPEQLSAYKHS 201

Query: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQH---SLVSPLRHPHVLFG 260
              +VQ PY+ +  V+ L+A+ + L + PAL       + +     SL   +R  H  + 
Sbjct: 202 LVLSVQTPYMIIVAVVLLVALLIMLTKFPALQSDDHSDATQSSFSASLARLVRVRHWRWA 261

Query: 261 VLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKL 320
           VLA F YVG + A  S+L+ Y ++ +I  M+   AAN++    +   IGRF G+ L+++ 
Sbjct: 262 VLAQFCYVGAQTACWSYLIRY-AIEEIPGMTPGFAANYLTGTMVCFFIGRFSGTWLISRF 320

Query: 321 SPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGE 380
           +P K+LA +A ++M L L +  T G V + ++     F SI +PTIFSLGI+ +G  T  
Sbjct: 321 APHKVLAAYALLSMILCLISAFTGGHVGLLALTLCSAFMSIQYPTIFSLGIKNLGQDTKY 380

Query: 381 ASSLLIMAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAYIVFYGLYGSR 431
            SS ++M I+GG IV  V G  +D  G +  A  +P LC+A I  +  + S+
Sbjct: 381 GSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELVPALCFAVIFIFARFRSQ 432


Lambda     K      H
   0.327    0.140    0.414 

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: 487
Number of extensions: 31
Number of successful extensions: 4
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: 442
Length of database: 436
Length adjustment: 32
Effective length of query: 410
Effective length of database: 404
Effective search space:   165640
Effective search space used:   165640
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 (21.7 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