GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_0562 Ga0059261_0562 Predicted
           ABC-type transport system involved in lysophospholipase
           L1 biosynthesis, ATPase component
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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