GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS22920 BWI76_RS22920 MFS
           transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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