GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Burkholderia phytofirmans PsJN

Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate BPHYT_RS01810 BPHYT_RS01810 sugar ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21390
         (340 letters)



>FitnessBrowser__BFirm:BPHYT_RS01810
          Length = 319

 Score =  187 bits (474), Expect = 4e-52
 Identities = 121/326 (37%), Positives = 188/326 (57%), Gaps = 38/326 (11%)

Query: 17  RRRLPTELSIFLVLIGIGLV-FEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQ 75
           ++ LP  L++   L+  GLV +E FG      SF   +          S+  L+++G+  
Sbjct: 2   KKNLPILLAL-AALVVFGLVRYEHFGSAYNITSFWRYN----------SMFALISVGMAF 50

Query: 76  VIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGA 135
           VIIT GIDLS G+V AL++++AA    TS +             W+ V+AG G GL  G 
Sbjct: 51  VIITGGIDLSVGTVAALASVVAAL---TSVYGG-----------WVAVLAGCGAGLAVGV 96

Query: 136 INGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDS-YTAIGHGAM-----PV 189
           +NG II    I PFI TL   + A G+A    +   VS+ ++S +   G G +     P 
Sbjct: 97  LNGLIITRLKILPFIVTLATSLGAHGVALLLGKNDAVSIAAESNFGNFGQGDLFGLPIPG 156

Query: 190 IIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGV 249
           I+ +V AV   +ALR T++G+++ AIGG+ +AAR  G+NV R LV+ Y+++GLLAG+AGV
Sbjct: 157 IVAVVAAVAGWLALRSTRFGRHSLAIGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGV 216

Query: 250 VASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVM------AS 303
           + +A+   GQ   G+ +EL AI+A V+GGT L GG G I  T+ G L+LG++       +
Sbjct: 217 ILAAQFGAGQPNEGVGWELFAISAVVLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFEN 276

Query: 304 GFTFVGVDAYIQDIIKGLIIVIAVVI 329
           G  F+ + AY Q +I+G+ +++ +V+
Sbjct: 277 GLGFISLSAYWQSVIRGVFLLLVIVL 302


Lambda     K      H
   0.326    0.140    0.394 

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: 244
Number of extensions: 13
Number of successful extensions: 3
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: 340
Length of database: 319
Length adjustment: 28
Effective length of query: 312
Effective length of database: 291
Effective search space:    90792
Effective search space used:    90792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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.

Links

Downloads

Related tools

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