GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Synechococcus elongatus PCC 7942

Align histidine transport ATP-binding protein hisP (characterized)
to candidate Synpcc7942_1414 Synpcc7942_1414 ATPase

Query= CharProtDB::CH_003210
         (257 letters)



>FitnessBrowser__SynE:Synpcc7942_1414
          Length = 241

 Score =  147 bits (372), Expect = 2e-40
 Identities = 95/225 (42%), Positives = 132/225 (58%), Gaps = 16/225 (7%)

Query: 13  KRYGEHEV----LKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVNGQT 68
           K YGE E     L  V  Q  AG+  +I+G+SGSGKST +  I  L++P+ G   ++G  
Sbjct: 16  KIYGEGETTVRALDHVDFQVRAGEYCAIMGASGSGKSTAMNLIGCLDRPTAGRYYLDGTD 75

Query: 69  INLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKQEA 128
              V D D     A +N+      ++  VFQ F+L   ++ +ENVM  P+   G+S+QE 
Sbjct: 76  ---VADLDDDALAAVRNR------KIGFVFQQFHLLPQLSAVENVM-LPMIYAGISQQER 125

Query: 129 RERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDPELV 188
           R+RAV  L +VG+ +R   K P  LSGGQQQRV+IARA+  +P +LL DEPT ALD +  
Sbjct: 126 RDRAVAALTQVGLAQRLDNK-PNQLSGGQQQRVAIARAIVNQPVLLLADEPTGALDSQTT 184

Query: 189 GEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEE 233
            EVL I  QL + G T+V+VTHE   A   +  VI+   G+I+ E
Sbjct: 185 EEVLNIFDQLHQRGITIVIVTHEAEVADR-AERVIWFRDGQIQRE 228


Lambda     K      H
   0.318    0.134    0.375 

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: 158
Number of extensions: 6
Number of successful extensions: 4
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: 257
Length of database: 241
Length adjustment: 24
Effective length of query: 233
Effective length of database: 217
Effective search space:    50561
Effective search space used:    50561
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: 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