GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BPHYT_RS29175 BPHYT_RS29175 ABC transporter ATP-binding protein

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



>FitnessBrowser__BFirm:BPHYT_RS29175
          Length = 390

 Score =  315 bits (806), Expect = 2e-90
 Identities = 169/365 (46%), Positives = 235/365 (64%), Gaps = 10/365 (2%)

Query: 2   ATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61
           A + +RN+    GA     ++N++L ++ GEF++L+GPSGCGKSTL++ IAGL  +T G+
Sbjct: 35  ANVAVRNLTIQLGANT--VIENLDLDVQAGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGS 92

Query: 62  IMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAK 121
           I I  +D++   PKDR IA+VFQSYALYPTMSV  N+ F L+I   P+A+I   VAR ++
Sbjct: 93  IEIAGEDMTWADPKDRRIALVFQSYALYPTMSVERNLSFALRINGTPKAEIARRVARASE 152

Query: 122 LLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181
           +LQ+  LL RKP QLSGGQ+QRVA+GRA+ R   ++LFDEPLSNLDAKLR E+R E+K +
Sbjct: 153 MLQLGPLLKRKPAQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQL 212

Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPM 241
           HQRL  T +YVTHDQ+EAMTL  ++AVM+ G+IQQFGTP E+Y  P N FVA+F+G+P M
Sbjct: 213 HQRLGATMIYVTHDQVEAMTLATRMAVMRGGVIQQFGTPAEVYARPDNLFVATFLGTPAM 272

Query: 242 NFVPLRLQRKDGRLVALLDSGQAR-CELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           N +  RL+ +DG L    +  +         TT A       +LG+R E + LA G    
Sbjct: 273 NLIKGRLETRDGALHFCTEHWRLDVSRYPFRTTPA--NGLPCVLGVRAEDVRLAEG---- 326

Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDAN 360
            +S  A+V + EP G   ++++  +  +V           +G+     FD + V LFD  
Sbjct: 327 -ASEHAKVSLVEPMGNHRVIWLDYHGVQVASIDQTKTPLAIGDAAAFSFDSTHVSLFDEA 385

Query: 361 TGERL 365
            G RL
Sbjct: 386 GGARL 390


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: 402
Number of extensions: 12
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: 386
Length of database: 390
Length adjustment: 30
Effective length of query: 356
Effective length of database: 360
Effective search space:   128160
Effective search space used:   128160
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