GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00890 in Burkholderia phytofirmans PsJN

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS04435 BPHYT_RS04435 ABC
           transporter
          Length = 646

 Score =  157 bits (398), Expect = 6e-43
 Identities = 94/301 (31%), Positives = 164/301 (54%), Gaps = 41/301 (13%)

Query: 9   IIGAVALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVG 67
           +  A+AL+ L +     GN + + + +  ++Y +L  GL+IVVGY G + LG+   + VG
Sbjct: 7   VASALALIALAVFPVLSGNPYYIHLLETIMIYAILLFGLDIVVGYTGQVSLGHAGLFGVG 66

Query: 68  AY----LFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123
           AY    LF  +  P +                    +  P+A L+ A FGA+L  P L++
Sbjct: 67  AYTAGVLFFKLGMPFI--------------------VTAPLAILITAAFGAILALPALRV 106

Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI 183
            G YLA+VTL FG I++I +N +D    LTNGP G      VK+       +  + G  +
Sbjct: 107 SGPYLAMVTLAFGTILQILINEMDF---LTNGPMG------VKI------PKPSLAGRPM 151

Query: 184 NSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGM 243
           N V  YY+L   L+V S+I+ +R+  S +GRA+ A+R+  IA+  MG++    K+ AF +
Sbjct: 152 NEVE-YYWLVAALLVASLIVVHRVLRSHLGRAFEALRDSPIASDCMGVSVYRYKVYAFVI 210

Query: 244 GASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEV 303
            A F G++G ++   + ++SP +++   +++ +  +++GG     G +LG+ ++  LP++
Sbjct: 211 SAGFAGLAGCLYSYSEQYISPNTYNFELTILFLLAIIMGGRKTRTGALLGSAIIVLLPKL 270

Query: 304 L 304
           L
Sbjct: 271 L 271


Lambda     K      H
   0.328    0.144    0.430 

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: 444
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 646
Length adjustment: 34
Effective length of query: 324
Effective length of database: 612
Effective search space:   198288
Effective search space used:   198288
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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