Alignments for a candidate for MFS-glucose in Clostridium tyrobutyricum FAM22553

GapMind for catabolism of small carbon sources

Alignments for a candidate for MFS-glucose in Clostridium tyrobutyricum FAM22553

Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_017751862.1 PN53_RS09365 sugar porter family MFS transporter

Query= TCDB::Q8NTX0
         (491 letters)



>NCBI__GCF_000816635.1:WP_017751862.1
          Length = 466

 Score =  382 bits (980), Expect = e-110
 Identities = 197/451 (43%), Positives = 295/451 (65%), Gaps = 8/451 (1%)

Query: 26  RKRLFYVALVATFGGLLFGYDTGVINGALNPMTR--ELGLTAFTEGVVTSSLLFGAAAGA 83
           +K L  ++++ATFG LLFGYD+GVINGAL  + R  +L LT  TEG+VTSSLL GAA GA
Sbjct: 10  KKFLRKISILATFGSLLFGYDSGVINGALTFIARKDQLNLTPLTEGLVTSSLLLGAAIGA 69

Query: 84  MFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVPVY 143
           +  G  SD +GR+K +  LA  FF  T+ C  +P+  ++++ R ++G+ VGG S VVP  
Sbjct: 70  VLMGHFSDKYGRKKVLKVLAAVFFFSTIGCSISPNAEIIIICRFIVGIGVGGVSVVVPTL 129

Query: 144 LAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAIAL 203
           LAE+AP +IRGSL  R++ MIV GQL A++ N I+GNVF  + G+WRYM+AI++IPA+ L
Sbjct: 130 LAEMAPTKIRGSLVSRDQFMIVTGQLLAYIFNGILGNVF-ENPGIWRYMIAISSIPAVVL 188

Query: 204 FFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSMGL 263
           +FGML VPE+PRWL   G+I +A  +L   R  + A AE+ +++     E ++   +   
Sbjct: 189 WFGMLVVPETPRWLASHGKIADALEILRQTREEQEAEAEIKEIQKNIEAESSLERATF-- 246

Query: 264 REILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGVIA 323
            + L   W+ RI+++G  + + QQ  G+N +MYYG  VL ++GF    ALIAN+  G+++
Sbjct: 247 -KELGIPWIRRIVIIGCLIAIIQQFAGVNVLMYYGTTVLEKSGFGVKTALIANIGNGIMS 305

Query: 324 VVGAFIALWMM-DRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLRPYVILTLVVVF 382
           VV ++I + ++ +R NRR  LI GY  TT++ + I I S     G    P+VI+ L ++F
Sbjct: 306 VVASWIYMHLLSNRCNRRPLLIIGYCGTTVTWLAITIVSHVLS-GSGTLPFVIVILTMIF 364

Query: 383 VGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIMEAVGLTGTF 442
           +   Q  L   TW++LSE+FPL +RG   G++ FF WI N  +GL FP ++   GL+ TF
Sbjct: 365 LAIDQATLGPLTWLLLSEIFPLRVRGMGYGVATFFNWIGNFAVGLTFPILIAYFGLSSTF 424

Query: 443 FMFAGIGVVALIFIYTQVPETRGRTLEEIDE 473
            +F  +GV+ +I     VPETRG++LE++++
Sbjct: 425 LIFVLLGVLCIICAIMVVPETRGKSLEQMED 455


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: 555
Number of extensions: 23
Number of successful extensions: 7
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: 466
Length adjustment: 34
Effective length of query: 457
Effective length of database: 432
Effective search space:   197424
Effective search space used:   197424
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources