GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Echvi_1871 in Bacteroides thetaiotaomicron VPI-5482

Align SSS sodium solute transporter (characterized, see rationale)
to candidate 349883 BT0355 Na+/glucose cotransporter (NCBI ptt file)

Query= uniprot:L0FZF3
         (547 letters)



>FitnessBrowser__Btheta:349883
          Length = 564

 Score =  266 bits (681), Expect = 1e-75
 Identities = 182/585 (31%), Positives = 302/585 (51%), Gaps = 67/585 (11%)

Query: 6   LDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQF 65
           LD +V   + L +I + + V R+K+    DS DYFL  +   W A+GAS+ ASNI +E  
Sbjct: 4   LDWLVIGVFFLALIGIIVWVVRQKQN---DSADYFLGGRDATWLAIGASIFASNIGSEHL 60

Query: 66  IGMSGSGFALGLAISTYE---WMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVR 122
           IG++G+G + G+A++ +E   WM    +L++   F+P Y +  +YTMP+FL RRY+ + R
Sbjct: 61  IGLAGAGASSGMAMAHWEIQGWM----ILILGWVFVPFYSRSMVYTMPEFLERRYNPQSR 116

Query: 123 TVMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGI-------IGLALFAMVYSIYG 175
           T++++  L+ YV   +   +Y G L  + + G+   +GI       IGL +   +Y+I+G
Sbjct: 117 TILSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFG 176

Query: 176 GLKAVAWTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEM 235
           G+K+V +T V+Q   L+ G L    L    +G  D  E + +      + +      G+ 
Sbjct: 177 GMKSVLYTSVLQTPILLLGSLIILVLGFKELGGWD--EMMRVCGAVTVNDY------GDT 228

Query: 236 MIPDGSGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFA 295
           M  +    + DA  + P L  LIG   I+   YW  +Q+I QR L+ K+  EA+ G +F 
Sbjct: 229 MT-NLIRSNDDA--NFPWLGALIGSA-IIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFG 284

Query: 296 GFLKLLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLL-HLLPPGL 354
            +LKLL   + +IPG+ A+ + QK   A     +     G A +D A+PTL+  LLP G+
Sbjct: 285 AYLKLLPVFLFLIPGMIAFALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGV 344

Query: 355 KGLAFAALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIA 414
           KGL    + AA++SSLAS+ NS++ +FTID YK  F     E K V IG+I  VV  I+ 
Sbjct: 345 KGLVVCGILAALMSSLASLFNSSAMLFTIDFYKR-FRPETPEKKLVGIGQIATVVIVILG 403

Query: 415 AIVAPQLRQL-DQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPL--- 470
            +  P +R + D  + Y+Q+    ++PG+ A F+ G  WK+T++   +   +  + +   
Sbjct: 404 ILWIPIMRSVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLT 463

Query: 471 ---------------SAAFKVITPNLPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAI 515
                           + FK +  ++ ++   G +FL   +++I +SL      ++  A 
Sbjct: 464 RLGAKVYYSNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSL----ATEAPTAE 519

Query: 516 EVDAELFSTSTKFKVGA-------------VLICGILVALYSVFW 547
           ++   +F T+TK +  A             V+I  I  A Y  FW
Sbjct: 520 KIQGLVFGTATKEQKAATRASWDHWDIIHTVIILAITGAFYWYFW 564


Lambda     K      H
   0.326    0.140    0.414 

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: 808
Number of extensions: 35
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 547
Length of database: 564
Length adjustment: 36
Effective length of query: 511
Effective length of database: 528
Effective search space:   269808
Effective search space used:   269808
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 (21.6 bits)
S2: 53 (25.0 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