GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Pseudomonas simiae WCS417

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__WCS417:GFF4321
          Length = 386

 Score =  199 bits (506), Expect = 1e-55
 Identities = 127/372 (34%), Positives = 199/372 (53%), Gaps = 13/372 (3%)

Query: 3   LALDSISKKVGA--QTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60
           L L +++K  GA     L ++ L+++ G   +L+G +  GK++LM  +AGL+  T G + 
Sbjct: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63

Query: 61  VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRL 118
           +  +DV+GM  +DR++AMV+Q +  YP+M V  NI   LK+R   + +IDA V  +A  L
Sbjct: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123

Query: 119 HIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA 178
            I+  L+R P +LSGGQQQRVA+ RALA+   + L DEPL NLD KLR E+R E+  +  
Sbjct: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183

Query: 179 AGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL 238
             ++T VY T +  EA+ LG   AV+ +G + Q+G   E+++ P +  VA     PPMN 
Sbjct: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243

Query: 239 MAASATAQGVRL-------QGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGD--VS 289
           +      +  RL       Q   EL L   +       + +G+R   + + A  GD   S
Sbjct: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASS 303

Query: 290 VAGVVELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRL 349
           +   V++ E +G DT V        +  +L      ++G  +TL  DP++  +F A+   
Sbjct: 304 IRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDANTGE 363

Query: 350 AQAPARPVTAQG 361
               A  + AQG
Sbjct: 364 RLGTASSLPAQG 375


Lambda     K      H
   0.318    0.133    0.375 

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: 287
Number of extensions: 15
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: 363
Length of database: 386
Length adjustment: 30
Effective length of query: 333
Effective length of database: 356
Effective search space:   118548
Effective search space used:   118548
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: 50 (23.9 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