GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BT0355 in Bacteroides thetaiotaomicron VPI-5482

Align Na+/glucose cotransporter (characterized, see rationale)
to candidate 349869 BT0341 Na+/glucose cotransporter (NCBI ptt file)

Query= uniprot:Q8AAV7
         (564 letters)



>lcl|FitnessBrowser__Btheta:349869 BT0341 Na+/glucose cotransporter
           (NCBI ptt file)
          Length = 523

 Score =  279 bits (713), Expect = 2e-79
 Identities = 158/465 (33%), Positives = 270/465 (58%), Gaps = 35/465 (7%)

Query: 1   MEALDWLVIGVFFLALIGIIVWVVRQKQNDSADYFLGGRDATWLAIGASIFASNIGSEHL 60
           ++ LDW ++  +FL LI I +W   +++  S+  FL      W  IG S++ +N+G   L
Sbjct: 6   LDTLDWGILIAYFLILIAIGIWASSKRKKGSS-LFLAEHSLRWHHIGFSMWGTNVGPSML 64

Query: 61  IGLAGAGASSGMAMAHWEIQGWM-ILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTIL 119
           I  A AG ++G+   ++    ++ I +L +VF P Y  S V T+PEF+ +R+   +R IL
Sbjct: 65  IASASAGFTTGIVSGNYAWYAFVFICLLAFVFAPRYLGSRVSTLPEFMGKRFGQSTRNIL 124

Query: 120 SVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGMK 179
           +  ++V+ +++ +A+T++AGG++ +QVF I         W +A+ L++++A +T+ GG+K
Sbjct: 125 AWYTIVTILISWLALTLFAGGVLIRQVFDIP-------MWQSALILLIISAFFTMLGGLK 177

Query: 180 SVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDDA 239
           +V YT+V Q  +L+L S  + ++G  ++GG   +  +  AV  + +     NL R NDD 
Sbjct: 178 AVAYTNVYQMILLILVSAALAIVGIYKVGG---ISALTDAVPADFW-----NLFRPNDDT 229

Query: 240 NFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIPG 299
            FPWL  ++G  ++G W+WCTDQ +VQ VL+ K+ KE + GT F  +LK+L V L+++PG
Sbjct: 230 AFPWLPIILGYPVMGVWFWCTDQSMVQPVLAAKSLKEGQLGTNFTGWLKILDVPLYILPG 289

Query: 300 MIAFALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGILAALMSS 359
           +I  AL             P L     N D A+ T+V  L P G+ GLV+  + AAL+S+
Sbjct: 290 IICLAL------------FPQL----ENPDEAYMTMVTHLFPVGMVGLVLAVLTAALVST 333

Query: 360 LASLFNSSAMLFTIDFY-KRFRPETPEKKLVGIGQIATVVIVILGILWIPIMRSV-GDVL 417
           + S  N+ + +FT+D Y K+ RP+  +K+++ +GQ+ TV   ++ ++    + S+ G  L
Sbjct: 334 IGSALNALSTVFTMDIYVKKIRPQAKQKEIIRVGQVVTVAGALISVIITIAIDSIHGLNL 393

Query: 418 YTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGL 462
           +   Q V   +AP +AA FL G+ WKRT+       L  G +  +
Sbjct: 394 FNVFQSVLGFIAPPMAAVFLFGVFWKRTTTLAANAALTVGTVFSI 438


Lambda     K      H
   0.328    0.142    0.454 

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: 908
Number of extensions: 55
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: 564
Length of database: 523
Length adjustment: 35
Effective length of query: 529
Effective length of database: 488
Effective search space:   258152
Effective search space used:   258152
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.

Links

Downloads

Related tools

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 preprint 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