GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Sphingomonas koreensis DSMZ 15582

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__Korea:Ga0059261_0562
          Length = 232

 Score =  124 bits (310), Expect = 2e-33
 Identities = 82/206 (39%), Positives = 125/206 (60%), Gaps = 10/206 (4%)

Query: 22  QVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLSGAKIDQKH 81
           ++L+G+  +I     ++I+GPSG GKS+ +  L+ LE  SGG + VAG+  +   +D+  
Sbjct: 28  EILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGEVSVAGI--AYGTLDEDG 85

Query: 82  L-RQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRALTYLDKVGLGTKA 140
           L R  R RVG+V Q F+L P +T  +N+ + P ++   P A A  RA   LD VGLG + 
Sbjct: 86  LARARRGRVGIVLQAFHLLPTMTAHENVAV-PLELAGAPDAFA--RAGAELDAVGLGHRL 142

Query: 141 DNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNVM--KQLAEEGMT 198
            +YP QLSGG++QRVAIAR +  +PEIL  DEPT  LD    G +++++  +Q A +  T
Sbjct: 143 THYPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIVDLLFDRQRAADA-T 201

Query: 199 MAVVTHEMQFAREVSNRVFFFNQGII 224
           + ++TH+   A E  +RV     G+I
Sbjct: 202 LLIITHDPALA-ERCDRVLTMRDGLI 226


Lambda     K      H
   0.321    0.139    0.397 

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: 153
Number of extensions: 7
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: 252
Length of database: 232
Length adjustment: 23
Effective length of query: 229
Effective length of database: 209
Effective search space:    47861
Effective search space used:    47861
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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