GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Pseudomonas fluorescens GW456-L13

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate PfGW456L13_4204 ABC transporter, ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4204
          Length = 329

 Score =  197 bits (501), Expect = 3e-55
 Identities = 117/288 (40%), Positives = 174/288 (60%), Gaps = 21/288 (7%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  + V+++ K F    V +  ++N  I+ GE   +LGPSG GK+T +R IAGL     G
Sbjct: 1   MSYVSVQHLQKSFAGTTVFS--DINCEIQKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGG 58

Query: 61  ELYFDDRLVASNGKLIVP--PEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIR 118
           ++  D       G  IVP  P+ R IGMVFQ++AL+PN+T  +N+AF L   K++ ++ R
Sbjct: 59  KILLD-------GADIVPVSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSR 111

Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178
           KRV EV K+++++     +P +LSGGQ QRVALAR+LV  P LLLLDEP S LDAR+R  
Sbjct: 112 KRVAEVLKLVELNDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKH 171

Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238
            R  ++++Q  LG+T + V+HD  +   ++DR+ ++ +GK+VQ G  E LY  PV +  A
Sbjct: 172 LREQIRQIQRELGLTTIFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAA 231

Query: 239 SLIGEINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKD 286
             IG  N L+    ++      L+ P++       I IRPE ++LS D
Sbjct: 232 GFIGNYNLLDADSASK-----LLQRPINKR-----IAIRPEAIELSLD 269


Lambda     K      H
   0.319    0.139    0.390 

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: 259
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: 353
Length of database: 329
Length adjustment: 28
Effective length of query: 325
Effective length of database: 301
Effective search space:    97825
Effective search space used:    97825
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 (21.7 bits)
S2: 49 (23.5 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