GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Burkholderia phytofirmans PsJN

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS15600 BPHYT_RS15600 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__BFirm:BPHYT_RS15600
          Length = 389

 Score =  244 bits (623), Expect = 4e-69
 Identities = 155/358 (43%), Positives = 207/358 (57%), Gaps = 52/358 (14%)

Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQIL----IYVMLAWGLNIVVGLAGLLDLG 165
           I  I ++  PM++ A  G         N+ +++L    +YVMLA GLN+VVG AGLLDLG
Sbjct: 28  ITAIFVIAAPMIIGAAGG---------NYWVRVLDFAMLYVMLALGLNVVVGFAGLLDLG 78

Query: 166 YVAFYAVGAYSYALLSSY----------------FGLSFWVLLPLSGIFAALWGVILGFP 209
           Y+AFYAVGAY+ ALLSS                   + F +++P +   AA +GVILG P
Sbjct: 79  YIAFYAVGAYTSALLSSPHLSSQFEWIAHLAPNGLHVPFLIIVPCAMAVAAFFGVILGAP 138

Query: 210 VLRLRGDYLAIVTLAFGEIIRLVLINW---TDVTKGTFGISSIPKATLFGIPFDATAGGF 266
            LRLRGDYLAIVTL FGEI+R+ L N     ++T G  GI+ I             AG F
Sbjct: 139 TLRLRGDYLAIVTLGFGEIVRIFLNNLDRPVNITNGPKGITGIDPVH---------AGDF 189

Query: 267 A-----KLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACR 321
           +      LF L   S Y   +LF L     +L  +V  RL+   IGRAW A+REDEIA +
Sbjct: 190 SLAQTHSLFGLQFPSVYSYYYLFVLA---ALLVIWVCTRLQHSRIGRAWAAIREDEIAAK 246

Query: 322 SLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSL 381
           ++GINT   KL AFA GA F G +G+ F + QGFVSPESF   ES V+LA VVLGGMG +
Sbjct: 247 AMGINTRNVKLLAFAMGASFGGLSGAMFGSFQGFVSPESFTLPESIVVLACVVLGGMGHI 306

Query: 382 TGIAIAAIVMVGGTELLREM--SFLKLIFGPDFT-PELYRMLIFGLAMVVVMLFKPRG 436
            G+ + A+++    E LR        ++FG +    E+ R L++ LAMV++ML++  G
Sbjct: 307 PGVILGAVLLAVLPEFLRSTMGPLQNMVFGHEIVDTEVIRQLVYALAMVLIMLYRSEG 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: 511
Number of extensions: 23
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