GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Methanobacterium lacus AL-21

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_013644894.1 METBO_RS06515 sugar porter family MFS transporter

Query= TCDB::P15729
         (468 letters)



>NCBI__GCF_000191585.1:WP_013644894.1
          Length = 453

 Score =  307 bits (786), Expect = 5e-88
 Identities = 167/455 (36%), Positives = 277/455 (60%), Gaps = 24/455 (5%)

Query: 16  FVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAFGAG 75
           FV+L++ + ++GG LFG+DT VI+GA+  +++ F   +    ++VS  L+G+ +GA  +G
Sbjct: 13  FVILVAAITSIGGLLFGYDTGVISGAILFIREDFLLSTTAQEVTVSAVLIGAVIGASISG 72

Query: 76  PIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEV 135
            +ADR+GR   ++LA+++F + +I S +   +   I  RV+ GI +G AS I P YIAEV
Sbjct: 73  ILADRYGRKIMIVLASIIFGIGAIFSSVSPNVNALIISRVVVGIAIGMASFIVPLYIAEV 132

Query: 136 SPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTELIP 195
           +P ++RG L SL QLAI  GI I+ + + + A    GS           WRWM    +IP
Sbjct: 133 APINIRGALVSLNQLAITLGIVISYMVDLYFA--PNGS-----------WRWMLGLAVIP 179

Query: 196 ALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGD-VPSRIEEIQATVSLDHKPRFS 254
           +L+  +  F +P SPR+L+++G   KA A+L K+ G D V   + EI+ T+ L+++ ++S
Sbjct: 180 SLILALGMFFMPPSPRWLISKGFESKAVAVLKKIRGIDNVDKEVNEIEQTLLLENEGKWS 239

Query: 255 DLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGF-TEEKSLLITVITGFI 313
           DLL  +  +   + IG+GL+A QQ  GIN + YY+  +    G  T   ++  TV  G +
Sbjct: 240 DLLEPK--IRSALIIGIGLAAFQQLTGINTVIYYAPTILEFAGLQTATVTIFATVGIGVV 297

Query: 314 NILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIAL 373
           N+L T+V+I  +D+ GR+PLLL G  GM ++LGI+ + F    ++   P LT + G +A+
Sbjct: 298 NVLLTVVSILLIDRLGRRPLLLAGITGMIVSLGIMGLAF----II---PGLTSSLGWLAV 350

Query: 374 VTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDTV 433
           +   LYV SF  S GPI W+++ E++  +IR  A+S+   + W  N +++ TF  +++ +
Sbjct: 351 ICLMLYVGSFAISLGPIFWLMIAEIYPLRIRGRAMSIVTMINWATNLVVAITFLTIIELL 410

Query: 434 GLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
           G    + LY   A +S+ F+++ V ETKGK+LE++
Sbjct: 411 GASGTFWLYGVIAVLSLLFVYYRVPETKGKSLEEI 445


Lambda     K      H
   0.325    0.140    0.430 

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: 544
Number of extensions: 36
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: 468
Length of database: 453
Length adjustment: 33
Effective length of query: 435
Effective length of database: 420
Effective search space:   182700
Effective search space used:   182700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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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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