GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Pseudomonas litoralis 2SM5

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein

Query= SwissProt::P02915
         (258 letters)



>NCBI__GCF_900105005.1:WP_090275879.1
          Length = 334

 Score =  174 bits (440), Expect = 3e-48
 Identities = 106/246 (43%), Positives = 143/246 (58%), Gaps = 16/246 (6%)

Query: 15  RYGGHEV--LKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINL 72
           R GG ++  L    L   AG V  IIG SG+GKST LR IN LE+PS G I+V G++   
Sbjct: 12  RVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNGRIMVAGEDTTA 71

Query: 73  VRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLG-LSKHDARE 131
           +  +           LR  R R+ M+FQHFNL S  TV +NV   P+++ G  ++     
Sbjct: 72  LNAEG----------LRRFRQRVGMIFQHFNLLSSATVADNVA-LPLRLAGSANRQQIAA 120

Query: 132 RALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGE 191
           R    L +VG+ + A  KYP  LSGGQ+QRV IARALA EP +LL DE TSALDP   G+
Sbjct: 121 RVASLLDRVGLSDHAS-KYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQ 179

Query: 192 VLRIMQQLAEE-GKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQ 250
           VL+++ ++  E   T+V++THEM   R V   V  +  G+I E+G    VF +PQ P  +
Sbjct: 180 VLQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTR 239

Query: 251 QFLKGS 256
            F+ GS
Sbjct: 240 SFVFGS 245


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: 222
Number of extensions: 9
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: 258
Length of database: 334
Length adjustment: 26
Effective length of query: 232
Effective length of database: 308
Effective search space:    71456
Effective search space used:    71456
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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