GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:349869
          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.

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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