GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntB in Burkholderia phytofirmans PsJN

Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate BPHYT_RS30450 BPHYT_RS30450 ABC transporter permease

Query= reanno::psRCH2:GFF2081
         (425 letters)



>FitnessBrowser__BFirm:BPHYT_RS30450
          Length = 619

 Score =  209 bits (531), Expect = 2e-58
 Identities = 125/419 (29%), Positives = 211/419 (50%), Gaps = 1/419 (0%)

Query: 1   MTVVVFLSSLLGFMTL-GMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAV 59
           + +++F   L+    L G+PIAF+  L     +       + ++   +  G     LL+V
Sbjct: 197 LNLLIFFVGLVALGVLSGVPIAFSFGLATFGYLALTTNTPMPVVVGRMDEGMSHLILLSV 256

Query: 60  PFFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALA 119
           P F+  G+L+   G++  +IA   +  GH RGGL YV + A  L++ +SGS  AD AA+A
Sbjct: 257 PLFVFLGQLIEMTGMAAAMIAFLASLLGHVRGGLSYVLVGAMYLVSGISGSKAADMAAVA 316

Query: 120 TLLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGL 179
            +L P M+ RG        L+AA G     IPPS+  +  G VTG SIS LF  GM+PG+
Sbjct: 317 PVLFPEMKARGAKPGDLVALLAATGAQTETIPPSLVLITLGSVTGVSISALFTGGMLPGI 376

Query: 180 IMGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPTE 239
           ++ + L +      RR D    ++A+  E  R LV    AL LP +I   +  G+ T TE
Sbjct: 377 VLAITLCIVVQWRYRREDMSSVKRATRGEILRKLVIAFPALALPFVIRAAVVEGIATATE 436

Query: 240 AAVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLPD 299
            + +   YA+    L+YR   W  L  +L   +  + +++ +  AAT  A+ +T +    
Sbjct: 437 VSTIGIAYAVLAGLLIYRRFEWKRLKPMLIDTATLSGAILLIIGAATAMAWALTQSGFSG 496

Query: 300 EIAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGV 359
           ++A  LG L     + M A + + + +G VL+  P I++ GP++ PIA    I  V++ +
Sbjct: 497 QLAQTLGALPGGAAMFMAASICMFVILGSVLEGIPAIVLFGPLMFPIARAMHIHDVHYAM 556

Query: 360 MFVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSIIT 418
           + +L   +GL  PP G        + R+  +  ++ ++ +    +  + ++ AVP I T
Sbjct: 557 VVILSMGVGLFAPPFGVGYYSACAVSRIHPDEGMKPILGYIAALMAGLIIVAAVPWIST 615


Lambda     K      H
   0.328    0.142    0.413 

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: 695
Number of extensions: 37
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: 425
Length of database: 619
Length adjustment: 35
Effective length of query: 390
Effective length of database: 584
Effective search space:   227760
Effective search space used:   227760
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: 52 (24.6 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