GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Caulobacter crescentus NA1000

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate CCNA_01506 CCNA_01506 cystine transport ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__Caulo:CCNA_01506
          Length = 246

 Score =  233 bits (593), Expect = 4e-66
 Identities = 124/240 (51%), Positives = 159/240 (66%), Gaps = 3/240 (1%)

Query: 9   ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68
           I    L+K+FG   VL GV   + P +V++IIGPSG GKST LRCL  LEP++ G L +A
Sbjct: 4   IDAKSLKKSFGDTPVLAGVDLAVVPGEVVAIIGPSGSGKSTLLRCLAGLEPLNDGDLTIA 63

Query: 69  GVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRAL 128
           GV   G     K L     RVG VFQ FNLFPH T L+N++  P  V R   A+A+ + L
Sbjct: 64  GVAAGGKTPLAKALNG---RVGFVFQSFNLFPHRTALENVIEGPIVVRREDPAKARAKGL 120

Query: 129 TYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNV 188
             L+KVGL  + D YP  LSGGQ+QR AIAR L M PE++LFDEPTSALDPELVGEVL V
Sbjct: 121 ALLEKVGLADRVDAYPSALSGGQQQRCAIARALAMDPEVILFDEPTSALDPELVGEVLAV 180

Query: 189 MKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLSR 248
           ++ LA E  TM +VTH+M FAR+V+ R  F + G+I E+G   ++  +P+ +R R FL+R
Sbjct: 181 IRDLAAEKRTMVIVTHQMDFARDVAERTIFMDGGVIVEQGPSRQLLASPREERTRRFLAR 240


Lambda     K      H
   0.321    0.139    0.397 

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: 197
Number of extensions: 7
Number of successful extensions: 2
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: 252
Length of database: 246
Length adjustment: 24
Effective length of query: 228
Effective length of database: 222
Effective search space:    50616
Effective search space used:    50616
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 (21.9 bits)
S2: 46 (22.3 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