GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Klebsiella michiganensis M5al

Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate BWI76_RS17580 BWI76_RS17580 MFS transporter

Query= TCDB::Q8NTX0
         (491 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS17580 BWI76_RS17580 MFS
           transporter
          Length = 479

 Score =  415 bits (1067), Expect = e-120
 Identities = 214/454 (47%), Positives = 300/454 (66%), Gaps = 4/454 (0%)

Query: 26  RKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGAAAGAMF 85
           RKRL  + LVATFGGLLFGYDTGVINGA + + + + LT  TEG+V S LL GAA G++F
Sbjct: 12  RKRLHQITLVATFGGLLFGYDTGVINGAFSSLKQYMALTPTTEGLVMSVLLIGAALGSVF 71

Query: 86  FGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVPVYLA 145
            G+ +D +GRRK ++ L+  FF+G ++   AP   V+++ R +LG AVGGAS   P +++
Sbjct: 72  GGKFADFFGRRKYLLFLSFIFFIGALMSALAPDITVLLISRFILGYAVGGASVTAPTFIS 131

Query: 146 ELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAIALFF 205
           E+AP E+RG L G NE+ IV+GQLAAF INAIIG ++GH   VWRYML +  IPAI LF 
Sbjct: 132 EVAPTEMRGKLTGLNEVAIVIGQLAAFAINAIIGILWGHLPDVWRYMLMVQTIPAICLFI 191

Query: 206 GMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSM-GLR 264
           GMLR PESPRWL+ + R +EA  +L+ IRPLERA  E  D+  L + E      S     
Sbjct: 192 GMLRSPESPRWLISKNRHEEALEILKQIRPLERATKEFNDITTLIKAEADKKLHSQNAFI 251

Query: 265 EILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGVIAV 324
            IL + W+ ++LLVG+     QQ TG+N IMYYG  +L  AGFSE  +LI NV  GV +V
Sbjct: 252 TILQTPWIFKLLLVGVIWAALQQTTGVNVIMYYGTEILSSAGFSERTSLICNVLNGVFSV 311

Query: 325 VG-AFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLRPYVILTLVVVFV 383
            G  F  L+++DR  R+T +I G++L    H++  IA V + +   ++   I  L  +FV
Sbjct: 312 GGMLFGVLFLVDRFKRKTIIIYGFALMATLHLI--IAGVDYTLVGDIKATAIWLLGAMFV 369

Query: 384 GSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIMEAVGLTGTFF 443
           G MQ  +   TWV+L+ELFPL  RG ++GISVFF+W+ NA +   FP +   +GL   F 
Sbjct: 370 GVMQGTMGFITWVVLAELFPLKFRGLSMGISVFFMWVMNAIVSYLFPLLQAKLGLGPVFL 429

Query: 444 MFAGIGVVALIFIYTQVPETRGRTLEEIDEDVTS 477
           +FA I  +A++F+ T +PET  ++LE+++E++++
Sbjct: 430 IFAAINYLAIVFVITALPETSNKSLEQLEEELSA 463


Lambda     K      H
   0.327    0.142    0.420 

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: 628
Number of extensions: 28
Number of successful extensions: 5
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: 491
Length of database: 479
Length adjustment: 34
Effective length of query: 457
Effective length of database: 445
Effective search space:   203365
Effective search space used:   203365
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: 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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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