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_RS04180 BPHYT_RS04180 sugar ABC transporter substrate-binding protein

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



>FitnessBrowser__BFirm:BPHYT_RS04180
          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:

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