GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Azospirillum brasilense Sp245

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate AZOBR_RS32415 AZOBR_RS32415 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__azobra:AZOBR_RS32415
          Length = 305

 Score =  207 bits (527), Expect = 2e-58
 Identities = 105/292 (35%), Positives = 178/292 (60%), Gaps = 11/292 (3%)

Query: 5   LQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVA 64
           LQQ++NGL +G VYAL+A+G+T+++G++ ++NFAHG++Y +GAF+G  +I +        
Sbjct: 8   LQQVINGLSIGCVYALMAIGFTLIFGVLNVVNFAHGEVYTIGAFVGLMVITAMAPPLLAV 67

Query: 65  LIVAMLATAILGVVIEFLAYRPLRHST----------RIAVLITAIGVSFLLEYGMVYLV 114
           + + +   A+ GV +E +A+RP R  T          R A L++++ VS +    M+++ 
Sbjct: 68  VPLVLAVGAVSGVGLERIAFRPFRRFTDEASQKSRAMREATLLSSLAVSIMTREIMMHIF 127

Query: 115 GANTRAFPQAIQTVR-YDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSV 173
           G + +  P      +   +GPI + +  L+I   S +++  LQ ++ +T+ G  +RAVS 
Sbjct: 128 GGDMQGIPSGYLLQQPVAIGPIMVASGSLVIFATSAVMLGALQFLLYRTQTGLGIRAVSN 187

Query: 174 DSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLG 233
           +   A+ +GIN +RTI  TFA+GS L   AG+L+ LY  ++ P MG  PG+K+FVA V+G
Sbjct: 188 NQLGARYVGINTDRTIVTTFAVGSMLGATAGILVGLYDGAISPHMGFAPGVKAFVAMVMG 247

Query: 234 GIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285
           G+  IPGA     ++G+ E+ AT F  S ++D I Y +L++ L+  P G+ G
Sbjct: 248 GLSSIPGAVACALLLGVSESIATEFLSSGWKDLITYSLLVITLVFFPQGLFG 299


Lambda     K      H
   0.330    0.146    0.407 

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: 226
Number of extensions: 9
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: 292
Length of database: 305
Length adjustment: 27
Effective length of query: 265
Effective length of database: 278
Effective search space:    73670
Effective search space used:    73670
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: 48 (23.1 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