GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Halococcus hamelinensis 100A6

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_152416156.1 C447_RS11610 ATP-binding cassette domain-containing protein

Query= TCDB::Q9HT70
         (335 letters)



>NCBI__GCF_000336675.1:WP_152416156.1
          Length = 233

 Score =  148 bits (374), Expect = 1e-40
 Identities = 91/213 (42%), Positives = 122/213 (57%), Gaps = 4/213 (1%)

Query: 6   DVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVE 65
           DV KTY + G  + AL    L++  G    ++G SG+GKSTLL L+  L+ P+ G + V 
Sbjct: 5   DVRKTYDLGGT-VEALAGVSLSLADGSYTAVMGPSGSGKSTLLNLVGALDTPTDGTVEVA 63

Query: 66  GEDV-TALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSE 124
           G D+  A D E        +G +FQ FNLL      +N+A+PL  AG +SR     R +E
Sbjct: 64  GNDLGAATDDERAAIRGTEIGFVFQTFNLLPRSDAVENVALPLVFAG-WSRERRHERATE 122

Query: 125 LLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLL 184
           LL RVGL D     P QLSGGQ+QRV IARALA  P+++L DE T  +D +T A V+ LL
Sbjct: 123 LLDRVGLGDRRHHRPTQLSGGQRQRVAIARALAPDPAVVLADEPTGNVDTETGAGVMNLL 182

Query: 185 AEINRELKLTIVLITHEMDVIRRVCDQVAVMDG 217
           A  N +   TI+L+TH  ++       V V DG
Sbjct: 183 AAAN-DRGTTILLVTHSREIAEHADRIVTVRDG 214


Lambda     K      H
   0.322    0.138    0.393 

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: 193
Number of extensions: 14
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: 335
Length of database: 233
Length adjustment: 26
Effective length of query: 309
Effective length of database: 207
Effective search space:    63963
Effective search space used:    63963
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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