GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS00415 BPHYT_RS00415 sugar ABC transporter substrate-binding protein

Query= reanno::WCS417:GFF4324
         (428 letters)



>FitnessBrowser__BFirm:BPHYT_RS00415
          Length = 422

 Score =  404 bits (1037), Expect = e-117
 Identities = 207/417 (49%), Positives = 263/417 (63%), Gaps = 10/417 (2%)

Query: 10  AISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAGGGG 69
           A+ +A++    A  A     VEV+H+WTSGGE  +  VLK  +++ G  WKD AVAGGGG
Sbjct: 15  ALGVAAVL---ACGAARSAEVEVLHYWTSGGEAKSAQVLKQMLDEKGDTWKDFAVAGGGG 71

Query: 70  ATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKKVSD 129
             AMT LK+R +AGNPP  AQIKGP IQEW   G+L +  + DVAK E WD L+  ++S 
Sbjct: 72  GNAMTALKTRVIAGNPPAAAQIKGPAIQEWGDEGVLVS--INDVAKREGWDKLIPPQISG 129

Query: 130 TVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIPLAH 189
            +KY+G YVA PVN+HRVN LWIN +  KK    + P T  EF+   + L+ AG  P+A 
Sbjct: 130 IMKYKGQYVAAPVNVHRVNRLWINADALKKVN-AQPPATWDEFFRTAEALQKAGITPVAI 188

Query: 190 GGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDVDGK 249
           GGQ WQD+  FE V L V GA  Y+KA V LD   L GP MVKAL   KK+  Y D    
Sbjct: 189 GGQQWQDAETFETVALGVGGAAFYEKAFVQLDQSTLRGPTMVKALETFKKIKAYTDKAQT 248

Query: 250 GQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNIDSLA 309
           G+DWNL  G VI+GKA MQ MGDWAK E++ A KV GKDY CV  PG+  A+T+N+DS A
Sbjct: 249 GRDWNLATGMVISGKAAMQFMGDWAKGEFSVAGKVPGKDYLCVPAPGSQNAYTFNVDSFA 308

Query: 310 VFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQTAAK 369
            FK +      GQ+D+A ++L   FQ++F++NKGSIPVR      MD   FD+CAQ +A 
Sbjct: 309 FFKVRSADVEKGQKDLASLLLSPKFQEIFNLNKGSIPVRQG----MDLSKFDTCAQRSAA 364

Query: 370 DFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIKS 426
           DF +    G L PS AH+M  T AV+GAF+DV+ N+ ND        A KL  A K+
Sbjct: 365 DFTSAQAKGTLVPSWAHDMVDTPAVEGAFYDVIGNFWNDDNESAQQAADKLAVAAKT 421


Lambda     K      H
   0.314    0.131    0.388 

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: 549
Number of extensions: 22
Number of successful extensions: 4
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: 428
Length of database: 422
Length adjustment: 32
Effective length of query: 396
Effective length of database: 390
Effective search space:   154440
Effective search space used:   154440
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: 42 (22.0 bits)
S2: 51 (24.3 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