GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Burkholderia phytofirmans PsJN

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS31745 BPHYT_RS31745 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__BFirm:BPHYT_RS31745
          Length = 389

 Score =  256 bits (653), Expect = 1e-72
 Identities = 150/354 (42%), Positives = 208/354 (58%), Gaps = 44/354 (12%)

Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQIL----IYVMLAWGLNIVVGLAGLLDLG 165
           +  I +   P+++ A  G         N+G+++L    +YVMLA GLNIVVG AGLLDLG
Sbjct: 28  LTAIGVTALPLLIGAAAG---------NYGVRVLDFAMLYVMLALGLNIVVGFAGLLDLG 78

Query: 166 YVAFYAVGAYSYALLSSY----------------FGLSFWVLLPLSGIFAALWGVILGFP 209
           Y+AFYAVGAY+ ALL+S                 F   +W ++P++ + AA+ G+ LG P
Sbjct: 79  YIAFYAVGAYTAALLTSPHLAAHFEWIGHMWPSGFHAPYWFVMPVAMVLAAIAGICLGAP 138

Query: 210 VLRLRGDYLAIVTLAFGEIIRLVLINW---TDVTKGTFGISSIPKATLFGIPFDATAGGF 266
            LRLRGDYLAIVTL FGEI+R+ + N     ++T G  GI+ +   T+ G     T    
Sbjct: 139 TLRLRGDYLAIVTLGFGEIVRIFMNNLDRPVNITNGPQGITGVAPVTVAGFNLSET---- 194

Query: 267 AKLFHLPISSAYYKIFLFYLILALC-MLTAYVTIRLRRMPIGRAWEALREDEIACRSLGI 325
               H  +   +  ++++Y +  LC +L  +V  RL+   IGRAW A+REDEIA +++GI
Sbjct: 195 ----HAFLGFQFTTVYMYYYVFVLCSLLVVWVCTRLQHSRIGRAWAAIREDEIAAKAMGI 250

Query: 326 NTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIA 385
           NT   KL AFA GA F G +G+ FA  QGFVSPESF   ES  +LA VVLGGMG + G+ 
Sbjct: 251 NTRNVKLLAFAMGASFGGLSGAMFAGFQGFVSPESFTLWESVTVLACVVLGGMGHIPGVI 310

Query: 386 IAAIVMVGGTELLRE--MSFLKLIFGPDFT-PELYRMLIFGLAMVVVMLFKPRG 436
             A+++    E+LR         IFG      E+ R L++GLAMV++ML +P G
Sbjct: 311 FGAVLLAILPEILRSTMTPLQNAIFGHVIVDTEVIRQLLYGLAMVIIMLRRPEG 364


Lambda     K      H
   0.330    0.145    0.432 

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: 514
Number of extensions: 27
Number of successful extensions: 4
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: 463
Length of database: 389
Length adjustment: 32
Effective length of query: 431
Effective length of database: 357
Effective search space:   153867
Effective search space used:   153867
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 (21.8 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