GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Paraburkholderia bryophila 376MFSha3.1

Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_00166 H281DRAFT_00166 carbohydrate ABC transporter substrate-binding protein, CUT1 family

Query= uniprot:A0A165KPY4
         (416 letters)



>FitnessBrowser__Burk376:H281DRAFT_00166
          Length = 415

 Score =  438 bits (1126), Expect = e-127
 Identities = 238/412 (57%), Positives = 284/412 (68%), Gaps = 8/412 (1%)

Query: 8   AAVAVGLAAAMSA--SAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGD 65
           A  A GL   +SA  +A  VEVLH+WTSGGE+K+V  LK  M  +G+TW+DFAVAGG G 
Sbjct: 9   ALCAAGLMCGVSAVQAAESVEVLHWWTSGGESKAVGVLKDDMTKQGYTWKDFAVAGGAGA 68

Query: 66  SAMTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMK 125
           +AMT LK++VISGN PSAAQ KGP IQ+WAS+GVL  +D++A    W + LP  +  +M 
Sbjct: 69  AAMTALKTQVISGNAPSAAQIKGPLIQDWASQGVLVPIDSVAG--DWKKNLPPEIDKIMH 126

Query: 126 YKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQ 185
             G YVAAP +VHRVNW++ +  AL KAG   +P TW EFFA ADK+KAAG+ P+A GGQ
Sbjct: 127 ADGHYVAAPFSVHRVNWLYINKAALDKAG-GKVPTTWPEFFAVADKMKAAGIQPIAMGGQ 185

Query: 186 NWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRD 245
            WQD T +E VVL  G A FY+ ALV LD   LTSD M    +T R+I+GY D G  GRD
Sbjct: 186 PWQDLTLWEDVVLSQG-ADFYKKALVDLDEKTLTSDKMVGVFDTVRKIQGYFDAGRTGRD 244

Query: 246 WNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFK 305
           WNLATAM+I GKAG Q MGDWAKGEF  AGK  G D++CAA PG+  A+TFNVDSF+ F+
Sbjct: 245 WNLATAMVINGKAGMQFMGDWAKGEFANAGKKSGSDYVCAAVPGTEKAYTFNVDSFVFFQ 304

Query: 306 LK-DAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDTA 364
            K   AA   Q  LA +IMSP FQE F+LNKGSIPVR G  M KFDDCAK S  D     
Sbjct: 305 QKGQKAATPGQLALAKTIMSPEFQEQFSLNKGSIPVRLGVSMAKFDDCAKKSYADEQVAI 364

Query: 365 KSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKTK 416
           KSGG VPS AHGMA   A  GAI DVV++F N  + S   A+  +A AAKTK
Sbjct: 365 KSGGYVPSLAHGMAQPDAAAGAISDVVTKFMNSQQDS-KSAVAALAKAAKTK 415


Lambda     K      H
   0.315    0.128    0.383 

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: 616
Number of extensions: 40
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 416
Length of database: 415
Length adjustment: 31
Effective length of query: 385
Effective length of database: 384
Effective search space:   147840
Effective search space used:   147840
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 (21.6 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