GapMind for catabolism of small carbon sources

 

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

Align glucose transporter, ATPase component (characterized)
to candidate 350090 BT0562 putative ABC transporter ATP-binding protein (NCBI ptt file)

Query= reanno::Phaeo:GFF3641
         (260 letters)



>lcl|FitnessBrowser__Btheta:350090 BT0562 putative ABC transporter
           ATP-binding protein (NCBI ptt file)
          Length = 489

 Score = 97.4 bits (241), Expect = 5e-25
 Identities = 65/220 (29%), Positives = 118/220 (53%), Gaps = 8/220 (3%)

Query: 12  ATPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGE 71
           A P++E++ ++ SFG   AVDH+S  +  GE+ G LG NGAGK+T +++L G  +  +G 
Sbjct: 244 AAPVIEVEQLTKSFGHFTAVDHISFQVQRGEIFGFLGANGAGKTTAMRMLCGLSRPTSGV 303

Query: 72  IRVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEA 131
            +V G   +I    +    +I  + Q  +L ++L    N+   R     +G+  +  +E 
Sbjct: 304 GKVAG--YDIFREAEQVKRHIGYMSQKFSLYEDLKVWENI---RLFAGIYGM-KEMEIEE 357

Query: 132 ECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQM 191
           +  +++ RL    ++    V  L  G +Q +A + +++   KI+ +DEPT  + P   + 
Sbjct: 358 KTDELLERLGFADER-DTLVKNLPLGWKQKLAFSVSIFHEPKIVFLDEPTGGVDPATRRQ 416

Query: 192 VAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQL 231
             ELI Q   +GI +F+  H ++   E C+R S+M +GQ+
Sbjct: 417 FWELIYQAADRGITVFVTTHYMDEA-EYCNRISIMVDGQI 455



 Score = 95.9 bits (237), Expect = 1e-24
 Identities = 69/225 (30%), Positives = 121/225 (53%), Gaps = 20/225 (8%)

Query: 14  PLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIR 73
           P+V +K+IS S+G ++A+  VS  +  GEV GL+G +GAGKSTL ++L+     D G   
Sbjct: 6   PIVVVKEISKSYGKVEALKEVSFAVEQGEVFGLIGPDGAGKSTLFRILTTLLLADKGTAT 65

Query: 74  VNGDKVEITNPRDARSH-----NIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSA 128
           VNG  V +T+ +  R+         ++YQ L++ +NL+  + +F    +   + L+ D  
Sbjct: 66  VNGLDV-VTDYKQIRTKVGYMPGRFSLYQDLSVEENLEFFATVF-HTLIQENYDLIKD-- 121

Query: 129 MEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHE 188
                  I  ++ P F+K      ALSGG +Q +A++ ++     IL +DEPT  + P  
Sbjct: 122 -------IYQQIEP-FKK--RRAGALSGGMKQKLALSCSLIHKPDILFLDEPTTGVDPVS 171

Query: 189 TQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVG 233
            +   ++++ L+ QGI I ++   +      CDR + + +GQ+ G
Sbjct: 172 RKEFWQMLRNLRKQGITI-IVSTPIMDEARQCDRIAFINHGQVHG 215


Lambda     K      H
   0.317    0.135    0.373 

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: 248
Number of extensions: 13
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 489
Length adjustment: 29
Effective length of query: 231
Effective length of database: 460
Effective search space:   106260
Effective search space used:   106260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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