GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Dechlorosoma suillum PS

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Dsui_2068 Dsui_2068 ABC-type metal ion transport system, ATPase component

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__PS:Dsui_2068
          Length = 278

 Score =  240 bits (613), Expect = 3e-68
 Identities = 125/227 (55%), Positives = 165/227 (72%), Gaps = 1/227 (0%)

Query: 7   VHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEG 66
           V K++R    +   + PT L++  G+I G+IG SGAGKSTLLRL N LE P  G+++V G
Sbjct: 16  VSKSFRTPDGQQVGVHPTDLDVAPGEIHGIIGFSGAGKSTLLRLANLLERPDAGQVVVHG 75

Query: 67  EDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELL 126
           +D+  L    LR  RQR+GMIFQHFNLL ++TVADN+A PLR+AG    A ++ RV   L
Sbjct: 76  QDLMTLSPADLRTARQRIGMIFQHFNLLHNRTVADNVAFPLRIAGA-DEARINERVKTCL 134

Query: 127 ARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAE 186
             VGLS+ A  YPAQLSGGQKQRV IARALA  P +LL DE TSALDP+TT S+L++LA+
Sbjct: 135 EFVGLSEKAGVYPAQLSGGQKQRVAIARALAPEPHVLLADEPTSALDPRTTQSLLEVLAD 194

Query: 187 INRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHP 233
           +NR L +TI+L++HEM VIRR+C +V+VM+ G IVE+  +A+  + P
Sbjct: 195 VNRRLGVTILLVSHEMGVIRRLCHRVSVMEAGQIVERLTIANGRIPP 241


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: 301
Number of extensions: 11
Number of successful extensions: 2
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: 278
Length adjustment: 27
Effective length of query: 308
Effective length of database: 251
Effective search space:    77308
Effective search space used:    77308
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: 48 (23.1 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