GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HP1174 in Alistipes indistinctus YIT 12060

Align Glucose/galactose porter (characterized)
to candidate WP_009134173.1 HMPREF9450_RS06960 L-fucose:H+ symporter permease

Query= TCDB::P0C105
         (412 letters)



>NCBI__GCF_000231275.1:WP_009134173.1
          Length = 441

 Score =  188 bits (477), Expect = 3e-52
 Identities = 121/407 (29%), Positives = 201/407 (49%), Gaps = 29/407 (7%)

Query: 28  LTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISY 87
           +T LFF WGF   + + ++     +F+++ T   L+Q  F+G YF ++ PA   +++ SY
Sbjct: 19  VTSLFFAWGFANDITNPMVKAFSKIFRMSTTDGALVQLAFYGGYFAMAFPAALFIRKFSY 78

Query: 88  KRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPET 147
           K GI+VGL + A G  +FIPA+   +Y  FL A F+L  G++ L+ ++NPY+  +G   T
Sbjct: 79  KSGILVGLALYACGALMFIPASKTGLYFPFLIAYFILTCGLSFLETSSNPYILSMGDEST 138

Query: 148 AASRLTLTQAFNSLGTTVAPVFGAVLILSAAT----------------DATVNAEADAVR 191
           A  RL L+QAFN +G+ +  +F A+  + A                  +A   A+ + + 
Sbjct: 139 ATRRLNLSQAFNPIGSLLG-MFCAMQFIQARMSPLDTAERAQLSDAEFEAVKAADLNVLI 197

Query: 192 FPYLLLALAFTVL-AIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGA 250
            PY+++ L    L  +IF    P +  +D      +     W       G I  F YVGA
Sbjct: 198 TPYVIVGLVILALFFLIFFTKMPKNGDKDHSMNLGRVLKRIWAIPRYREGVIAQFFYVGA 257

Query: 251 EVSVGSFLVNFLSDP-TVAGLSETDAAHHVAYFWGGAM----VGRFIGSAAMRYIDDGKA 305
           ++   +F++ + +   T  G+ E  A      +   AM    V RFI +  M+Y   G  
Sbjct: 258 QIMCWTFIIQYGTRVFTQTGMEEQAAEVLSQRYNIVAMAIFCVSRFICTFLMKYFSPGAL 317

Query: 306 LAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGIL 365
           L   A     L    +       M+ ++ +    S+MFPTI+ +AL GLG     G+  L
Sbjct: 318 LMTFAIAGSALTAGVIGFQNINGMYCLVGVSACMSLMFPTIYGIALEGLGDDAKFGAAGL 377

Query: 366 CLAIVGGAIVPLIQGALAD------AIGIHLAFLMPIICYAYIAFYG 406
            +AI+GG+I+P  Q A+ D         ++++F++P+IC+  I  YG
Sbjct: 378 IMAILGGSIMPPAQAAIIDQGMLFGLPAVNVSFILPLICFLVIIVYG 424


Lambda     K      H
   0.328    0.141    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: 538
Number of extensions: 32
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: 412
Length of database: 441
Length adjustment: 32
Effective length of query: 380
Effective length of database: 409
Effective search space:   155420
Effective search space used:   155420
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 24 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