GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Caulobacter crescentus NA1000

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD

Query= TCDB::Q88P35
         (384 letters)



>FitnessBrowser__Caulo:CCNA_00647
          Length = 261

 Score =  157 bits (396), Expect = 4e-43
 Identities = 86/216 (39%), Positives = 134/216 (62%), Gaps = 8/216 (3%)

Query: 2   ATLELRNVNKTY--GSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITG 59
           A L + NV  T+  GS   + L  + L I  GEF+ ++G SGCGKSTL+N +AGL  +T 
Sbjct: 4   AYLSIENVGVTFAKGSVRSEVLTGVDLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTT 63

Query: 60  GAILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGL-KIRKLPQAAID--EEV 116
           GA+++D Q+V+   P   D A+VFQ+++L P +SVREN+   + K+    ++A +  E V
Sbjct: 64  GAVILDRQEVNAPGP---DRAVVFQNHSLLPWLSVRENVSLAVDKVFGGVKSAAERKEWV 120

Query: 117 ARVAKLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176
               +L+++ H L ++PA++SGG +QRV + RAL+  PK+ L DEP   LDA  R  ++ 
Sbjct: 121 LHNLELVKMTHALDKRPAEISGGMKQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQD 180

Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDG 212
            +  +H  LK T + +THD  EA  L D++ +M +G
Sbjct: 181 SVMEIHSALKNTVLMITHDVDEATLLSDRIVMMTNG 216


Lambda     K      H
   0.320    0.137    0.391 

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: 213
Number of extensions: 7
Number of successful extensions: 3
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: 384
Length of database: 261
Length adjustment: 27
Effective length of query: 357
Effective length of database: 234
Effective search space:    83538
Effective search space used:    83538
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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