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_RS29670 AZOBR_RS29670 ABC transporter permease

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__azobra:AZOBR_RS29670
          Length = 290

 Score =  211 bits (536), Expect = 2e-59
 Identities = 108/288 (37%), Positives = 173/288 (60%), Gaps = 3/288 (1%)

Query: 5   LQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVA 64
           LQ L+N ++LG  YALL +G T+++GI++++NF HG++Y  GA++ Y L     +NFF++
Sbjct: 5   LQHLLNAVVLGGTYALLGIGLTLIFGIMRVVNFTHGELYTFGAYMAYMLAGMMGLNFFMS 64

Query: 65  LIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFPQA 124
           L +A +    LG +IEF   RPL+ +     ++  IG    ++ G   + G   ++ P  
Sbjct: 65  LAMAAVLGMALGALIEFTLLRPLKGADIDTTMLVMIGAGIAMQAGEQLVWGGVAKSVPSP 124

Query: 125 IQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGIN 184
             T    LG +S+   +L +LG++L+L+    +++ +TK+G AMRA   D D A LMG+N
Sbjct: 125 FPTEPVVLGSVSVGMNRLFVLGVALLLLGGFYLLINRTKLGVAMRATFQDPDTAALMGVN 184

Query: 185 VNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAALG 244
                + TFALGS LA  AG L+   +  + P MG    LK+F   +LGG+G IPGA +G
Sbjct: 185 RGLMYTLTFALGSGLAATAGALLGPIF-VVTPTMGDLVALKAFAIVILGGLGNIPGATIG 243

Query: 245 GFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292
           GFV+ L E F   +  S +RDA+ + +++ +LIVRP G+    +KE++
Sbjct: 244 GFVLALAEEFGAGYLSSGYRDAMGFLLIIAVLIVRPQGLFA--MKERI 289


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: 274
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: 290
Length adjustment: 26
Effective length of query: 266
Effective length of database: 264
Effective search space:    70224
Effective search space used:    70224
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