GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Burkholderia phytofirmans PsJN

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate BPHYT_RS19350 BPHYT_RS19350 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__BFirm:BPHYT_RS19350
          Length = 382

 Score =  203 bits (516), Expect = 7e-57
 Identities = 130/366 (35%), Positives = 189/366 (51%), Gaps = 12/366 (3%)

Query: 2   KKSLLSAVALTAMLAFSGNAWA----DVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINA 57
           K   L+  AL A ++ +G A A    DV +  AGP+TG  A +G   Q G   A  D+NA
Sbjct: 4   KMKQLAGAALVAAMSLAGTANAQSTEDVKVGFAGPMTGAQAHYGKDFQNGITLAVEDMNA 63

Query: 58  AGG-INGEQIKIEL--GDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAEN 114
               I G+Q++  L   DD +DP+ G +VA K   DG+K ++GHFNSG +IPAS +YA  
Sbjct: 64  TKPVIGGKQVRFVLDSADDQADPRTGTTVAQKLVDDGIKGMLGHFNSGTTIPASRIYANA 123

Query: 115 GILRNHPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQ 174
           GI         P+    G   TFR    D QQG++AG +        KIA+V D+T YGQ
Sbjct: 124 GIPEIAMAT-APEYTQQGFKTTFRMMTSDTQQGSVAGTFAVKTLGVKKIAIVDDRTAYGQ 182

Query: 175 GLADETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQ 234
           GLAD+ +KA  AAG   V  E  N    DF +++ K+K     +IY+GG  ++A  +++Q
Sbjct: 183 GLADQFEKAAKAAGGQIVDREYTNDKAVDFKSILTKLKSVQPDLIYYGGADSQAAPMVKQ 242

Query: 235 AADQGLKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTAN-PANKELVEKFKAAGFN 293
               G+KA L+ G+ + +     IAGDA  GT+ +    P    P  K+ V K+K   FN
Sbjct: 243 MKALGIKAPLMGGEMVHTPTFIQIAGDAANGTVASLAGLPLEEMPGGKDYVAKYKKR-FN 301

Query: 294 P--EAYTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIP 351
              + Y+ Y+Y     +  A K A S DP      + +         ++++D KGD K  
Sbjct: 302 EDVQTYSPYAYDGAMAMFDAMKKANSTDPAKYLPVLAKTSMPAVTSANLAYDSKGDLKNG 361

Query: 352 GYIMYE 357
           G  +Y+
Sbjct: 362 GITLYK 367


Lambda     K      H
   0.314    0.132    0.383 

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: 381
Number of extensions: 24
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: 381
Length of database: 382
Length adjustment: 30
Effective length of query: 351
Effective length of database: 352
Effective search space:   123552
Effective search space used:   123552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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