GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Sphingomonas koreensis DSMZ 15582

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Ga0059261_0562 Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__Korea:Ga0059261_0562
          Length = 232

 Score =  115 bits (287), Expect = 2e-30
 Identities = 77/219 (35%), Positives = 113/219 (51%), Gaps = 11/219 (5%)

Query: 4   LELRNVNKTYGAGLPDT--LKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61
           +  RNV  T G     T  LK I++ I  G  + ++GPSG GKS+LM  ++GLE  +GG 
Sbjct: 11  IRARNVTLTLGTREAPTEILKGIDVDIARGSSVAILGPSGSGKSSLMAILSGLERASGGE 70

Query: 62  IMI-----GDQDVSGMSPKDRD-IAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAE 115
           + +     G  D  G++   R  + +V Q++ L PTM+  EN+   L++   P  D  A 
Sbjct: 71  VSVAGIAYGTLDEDGLARARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGAP--DAFAR 128

Query: 116 VARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMR 175
                  + + H L   P QLSGG+QQRVA+ RA+A RP+I   DEP  NLD      + 
Sbjct: 129 AGAELDAVGLGHRLTHYPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLDGATSGAIV 188

Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGII 214
             +    +    T + +THD   A    D+V  M+DG+I
Sbjct: 189 DLLFDRQRAADATLLIITHDPALAERC-DRVLTMRDGLI 226


Lambda     K      H
   0.318    0.135    0.382 

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: 209
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: 386
Length of database: 232
Length adjustment: 27
Effective length of query: 359
Effective length of database: 205
Effective search space:    73595
Effective search space used:    73595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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