GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Burkholderia phytofirmans PsJN

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate BPHYT_RS32360 BPHYT_RS32360 spermidine/putrescine ABC transporter ATPase

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__BFirm:BPHYT_RS32360
          Length = 362

 Score =  201 bits (512), Expect = 2e-56
 Identities = 112/292 (38%), Positives = 171/292 (58%), Gaps = 18/292 (6%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M+ + ++N+SK +        A  N+ + +  G    +LGPSG GKTT L++IAG   PT
Sbjct: 1   MSFLTLQNISKRYGN----FTATSNLDLEVKRGELLALLGPSGCGKTTTLQMIAGFVTPT 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
           +G +  D   +++ R     PEKR I +VFQ++AL+P+MTV DN+ F L++ KV +   +
Sbjct: 57  TGSVILDGRDITTER-----PEKRAIGVVFQSYALFPHMTVSDNVGFGLEMRKVNRADRK 111

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
             + E  + + L+G+ +RYPKELSGGQ QR AIARA+   P++LLLDEP SNLDA++RE 
Sbjct: 112 KSIAESLDFVRLNGLDHRYPKELSGGQRQRVAIARAIAMKPELLLLDEPMSNLDAKLREE 171

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
               +R IQ+   +TT++V+HD  +   ++++  V+  GK AQI TP + YE P+T   +
Sbjct: 172 MHIELRAIQKRLDITTILVTHDQVEAMTMSDRIAVMHQGKIAQISTPFDAYERPSTPFTS 231

Query: 241 RLTGEINLIQAKIIENNAIIAN-------LKVPLNNMELKGQSNIVIGLRPD 285
              G  N +   ++  N   A        L VP     +KG  N+ I  RP+
Sbjct: 232 TFLGRTNALTGSVVGRNPRCAEVAIADKVLLVPHEGRSVKGTVNVYI--RPE 281


Lambda     K      H
   0.317    0.136    0.374 

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: 278
Number of extensions: 10
Number of successful extensions: 2
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: 371
Length of database: 362
Length adjustment: 30
Effective length of query: 341
Effective length of database: 332
Effective search space:   113212
Effective search space used:   113212
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: 49 (23.5 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