GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Escherichia coli BW25113

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__Keio:14400
          Length = 348

 Score =  230 bits (586), Expect = 5e-65
 Identities = 142/350 (40%), Positives = 208/350 (59%), Gaps = 20/350 (5%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           +ELRNV K +G+     + NI L+I +G+ + L+GPSGCGK+T++  +AGLE  + G I 
Sbjct: 7   VELRNVTKRFGSNT--VIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIF 64

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           I  +DV+  S + RDI MVFQSYAL+P MS+ EN+ +GLK+  +P+A++ A V     ++
Sbjct: 65  IDGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMV 124

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
            +E   +R   Q+SGGQQQRVA+ RAL  +PK+ LFDEPLSNLDA LR  MR +++ + +
Sbjct: 125 DLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQK 184

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243
           +   T++YVTHDQ EA  + D V VM  G I Q G+P+++Y  PA++F+ASF+G    N 
Sbjct: 185 QFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGD--ANL 242

Query: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLA-AGEGDSAS 302
            P      DG  V +      R  L   T   G+      +G+RPE I L+  GE     
Sbjct: 243 FPATF--SDG-YVDIYGYHLPR-PLHFGTQGEGM------VGVRPEAITLSDRGE----E 288

Query: 303 SIRAEVQVTEPTGPDTLVFVQLNDTKVCCRL-APDVAPQVGETLTLQFDP 351
           S R  ++     GP   V V+ +  ++  ++ A  + P VGE   L+  P
Sbjct: 289 SQRCVIRHVAYMGPQYEVTVEWHGQEILLQVNATRLQPDVGEQYYLEIHP 338


Lambda     K      H
   0.318    0.135    0.382 

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: 346
Number of extensions: 16
Number of successful extensions: 1
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: 386
Length of database: 348
Length adjustment: 30
Effective length of query: 356
Effective length of database: 318
Effective search space:   113208
Effective search space used:   113208
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 (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