GapMind for catabolism of small carbon sources

 

Aligments 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_RS04180 BPHYT_RS04180 sugar ABC transporter substrate-binding protein

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS04180 BPHYT_RS04180 sugar ABC
           transporter substrate-binding protein
          Length = 415

 Score =  365 bits (936), Expect = e-105
 Identities = 195/420 (46%), Positives = 254/420 (60%), Gaps = 12/420 (2%)

Query: 7   LAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAG 66
           L  A  +AS    SA  A +  ++ V+HWWTSGGE  A+ VLK  ++K G+ WKD AVAG
Sbjct: 5   LMSAAIVASTLATSAQVASAAESLSVLHWWTSGGESKAIRVLKDDMDKQGYEWKDFAVAG 64

Query: 67  GGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKK 126
           G GA AMT LK++ ++GN P  AQIKGP IQ+WA  G+L  D+ K       W + L  +
Sbjct: 65  GAGAAAMTALKTQVMSGNAPSAAQIKGPLIQDWADQGVL-VDIDKSATD---WKAQLPAQ 120

Query: 127 VSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIP 186
           ++ T+  +G YVA P ++HR+NWLWIN     K G  K PTT  EF+A  DK +AAG  P
Sbjct: 121 INKTMMSKGHYVAAPFSVHRINWLWINKAALDKVG-GKPPTTWPEFFALADKFRAAGITP 179

Query: 187 LAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDV 246
           +A GGQPWQD T++E VVLS  GAD Y+KA++DLD   LT P+M++     +K+  Y D 
Sbjct: 180 VARGGQPWQDMTIWETVVLS-QGADFYRKAMIDLDQKTLTSPQMLQVFQTARKIQGYFDK 238

Query: 247 DGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNID 306
              G+DWNL    VING  GMQ MGDWAK E+  A K A  DY C A PGT  AFTY +D
Sbjct: 239 GSTGRDWNLATAMVINGSGGMQFMGDWAKGEFANANKKADVDYICAAAPGTSNAFTYTVD 298

Query: 307 SLAVFKQKDKGTAA-GQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQ 365
           S   F+Q  K  A  GQ  +AK ++   FQ+ FS+ KGSIPVR D+   MD   FD+CA+
Sbjct: 299 SFVFFQQNGKKEATLGQLALAKTIMSPAFQEQFSLYKGSIPVRQDV--SMDK--FDACAK 354

Query: 366 TAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIK 425
            +  D     K+    PS A     + A +GA  DVVT ++N    DP +  +K+ AA K
Sbjct: 355 KSYADEQTTIKSNTFFPSFAFGDVQSSATEGAITDVVTGFMNS-NEDPQEAMRKVAAAAK 413


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: 511
Number of extensions: 24
Number of successful extensions: 6
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: 415
Length adjustment: 32
Effective length of query: 396
Effective length of database: 383
Effective search space:   151668
Effective search space used:   151668
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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