GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Escherichia coli BW25113

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate 14789 b0652 glutamate and aspartate transporter subunit (NCBI)

Query= SwissProt::P02915
         (258 letters)



>FitnessBrowser__Keio:14789
          Length = 241

 Score =  221 bits (562), Expect = 1e-62
 Identities = 119/243 (48%), Positives = 164/243 (67%), Gaps = 12/243 (4%)

Query: 11  DLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNI 70
           ++ K YG  +VL   S + + G+V+ + G SGSGKST ++ +N LE   +G I V+G  +
Sbjct: 6   NVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDGIVV 65

Query: 71  NLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDAR 130
           N   DK        K  L  LR+R+ MVFQHF L+ H++++EN+  A ++VL   K  AR
Sbjct: 66  N---DK--------KTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAR 114

Query: 131 ERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVG 190
           E+ALK L +VG+   A  K+P  LSGGQQQRV+IARAL M+P  +LFDEPTSALDPE++ 
Sbjct: 115 EKALKLLERVGLSAHAN-KFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMIN 173

Query: 191 EVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQ 250
           EVL +M +LA EG TM+VVTHEMGFAR V++ VIF+ +GKI E+   +  F +P+S R +
Sbjct: 174 EVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAK 233

Query: 251 QFL 253
            FL
Sbjct: 234 DFL 236


Lambda     K      H
   0.319    0.136    0.383 

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: 179
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: 258
Length of database: 241
Length adjustment: 24
Effective length of query: 234
Effective length of database: 217
Effective search space:    50778
Effective search space used:    50778
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 (21.7 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