GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Erythrobacter marinus HWDM-33

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_047094318.1 AAV99_RS11970 ABC transporter ATP-binding protein

Query= SwissProt::P02915
         (258 letters)



>NCBI__GCF_001013305.1:WP_047094318.1
          Length = 240

 Score =  132 bits (331), Expect = 9e-36
 Identities = 90/230 (39%), Positives = 133/230 (57%), Gaps = 18/230 (7%)

Query: 2   MSENKLHVID-LHKRYG----GHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLE 56
           M+++KL  ++ + K +G      + LKGV ++   GD ++I+G SGSGKST +  +  L+
Sbjct: 1   MTQHKLIELEGITKTFGKGPAAFQALKGVDMKIDRGDFVAIMGPSGSGKSTTMNILGCLD 60

Query: 57  KPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTR-LTMVFQHFNLWSHMTVLENVM 115
            P++G          + R +  +++   ++Q  LLR R L  VFQ FNL +  T LENV 
Sbjct: 61  VPTDG----------IFRFRGIEVQALTRDQRSLLRRRYLGFVFQGFNLLARTTALENV- 109

Query: 116 EAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVL 175
           E P+   G +K   R  A + L KVG+   A    P  LSGGQQQRV+IARAL  +PDVL
Sbjct: 110 ELPLLYRGETKKQRRIAAERSLDKVGLLPWASHT-PAELSGGQQQRVAIARALVTDPDVL 168

Query: 176 LFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIF 225
           L DEPT  LD E   E++ ++  L++ G T+++VTHE   A +  + V F
Sbjct: 169 LADEPTGNLDTERSLEIMELLTDLSDTGITVLMVTHEEEMAEYARTIVHF 218


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: 134
Number of extensions: 9
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: 240
Length adjustment: 24
Effective length of query: 234
Effective length of database: 216
Effective search space:    50544
Effective search space used:    50544
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 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