GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Sphingomonas koreensis DSMZ 15582

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__Korea:Ga0059261_0562
          Length = 232

 Score =  144 bits (362), Expect = 3e-39
 Identities = 88/215 (40%), Positives = 125/215 (58%), Gaps = 7/215 (3%)

Query: 10  TYRVAGREIPA--LQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGE 67
           T  +  RE P   L+   ++I  G    ++G SG+GKS+L+ +++ LE  SGG + V G 
Sbjct: 17  TLTLGTREAPTEILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGI 76

Query: 68  DVTALDAEGLRRFRQ-RVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELL 126
               LD +GL R R+ RVG++ Q F+LL + T  +N+A+PL LAG     +  AR    L
Sbjct: 77  AYGTLDEDGLARARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGA---PDAFARAGAEL 133

Query: 127 ARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAE 186
             VGL      YP QLSGG++QRV IARA+A RP IL  DE T  LD  T+ +++ LL +
Sbjct: 134 DAVGLGHRLTHYPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIVDLLFD 193

Query: 187 INRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIV 221
             R    T+++ITH+  +  R CD+V  M  G IV
Sbjct: 194 RQRAADATLLIITHDPALAER-CDRVLTMRDGLIV 227


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: 217
Number of extensions: 14
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: 335
Length of database: 232
Length adjustment: 25
Effective length of query: 310
Effective length of database: 207
Effective search space:    64170
Effective search space used:    64170
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 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