GapMind for catabolism of small carbon sources

 

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

Align Hexuronate transporter (characterized)
to candidate H281DRAFT_03828 H281DRAFT_03828 MFS transporter, ACS family, hexuronate transporter

Query= SwissProt::P0AA78
         (432 letters)



>FitnessBrowser__Burk376:H281DRAFT_03828
          Length = 429

 Score =  212 bits (539), Expect = 2e-59
 Identities = 121/404 (29%), Positives = 205/404 (50%), Gaps = 7/404 (1%)

Query: 8   RWYMIALVTLGTVLGYLTRNTVAAAAPTLMEELNISTQQYSYIIAAYSAAYTVMQPVAGY 67
           RW + AL+   TV+ Y+ R  +   AP L  ++  S  QY  I+ A+SA Y V     G 
Sbjct: 16  RWTVCALLFFATVINYMDRQILGLLAPLLQHDIGWSQVQYGRIVIAFSAFYAVGLLCFGR 75

Query: 68  VLDVLGTKIGYAMFAVLWAVFCGATALAGSWGGLAVARGAVGAAEAAMIPAGLKASSEWF 127
           ++D LGT+I YA+  ++W++     A  GS  G A+ R  +G  E    PA +K ++EWF
Sbjct: 76  IVDWLGTRISYALAMLIWSIAAMLHAAVGSVTGFAMVRALLGIGEGGNFPAAIKTTAEWF 135

Query: 128 PAKERSIAVGYFNVGSSIGAMIAPPLVVWAIVMHSWQMAFIISGALSFIWAMAWLIFYK- 186
           P +ER++A G FN G++IGA+ AP ++    +   W+ AF+I GAL  +W   W  FY+ 
Sbjct: 136 PRRERALATGIFNSGANIGAVFAPAIIPPLALAFGWRSAFVIIGALGIVWLAVWFAFYRS 195

Query: 187 -HPRDQKHLTDEERDYIINGQEAQHQVSTAKKMSVGQILRNRQFWGIALPRFLAEPAWGT 245
             PR      +E RD +   +      + A+    G ++R RQ W   + +FL +P W  
Sbjct: 196 AEPRSHDDDLEEARDEV---EALDAANANARAPGWGVLIRKRQTWAFLIGKFLTDPVWWF 252

Query: 246 FNAWIPLFMFKVYGFNLKEIAMFAWMPMLFADLGCILGGYLPPLFQRWFGVNLIVSRKMV 305
           +  W+P ++ +  G +++ I +          +G I GG+L     R  G ++  +RK  
Sbjct: 253 YLFWLPKWLNESRGMDMQHIGLPLVCIYAMTTVGSIGGGWLSSALLR-AGWSVNAARKTA 311

Query: 306 VTLGAVLMIGPGMIGLFTNPYVAIMLLCIGGFAHQALSGALITLSSDVFGRNEVATANGL 365
           + + A  ++    +    N + A+ ++ +   AHQ  S  L T +SD+F +  +    G+
Sbjct: 312 MFICACCVLPIAFVSQVDNLWGAVAIVGLAAAAHQGWSANLFTTASDLFPKRALGAVVGI 371

Query: 366 TGMSAWLASTLFALVVGALADTIG-FSPLFAVLAVFDLLGALVI 408
            GM+  +   LF+ V+G +    G +  LFA+ A+  L+   V+
Sbjct: 372 GGMAGSIGGVLFSEVIGQVLQRTGHYWVLFAIGALAYLIAFAVM 415


Lambda     K      H
   0.326    0.138    0.437 

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: 618
Number of extensions: 29
Number of successful extensions: 4
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: 432
Length of database: 429
Length adjustment: 32
Effective length of query: 400
Effective length of database: 397
Effective search space:   158800
Effective search space used:   158800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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