GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Azospirillum brasilense Sp245

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate AZOBR_RS00675 AZOBR_RS00675 ABC transporter permease

Query= uniprot:B2TBJ8
         (250 letters)



>FitnessBrowser__azobra:AZOBR_RS00675
          Length = 229

 Score =  222 bits (566), Expect = 4e-63
 Identities = 106/226 (46%), Positives = 160/226 (70%)

Query: 4   DFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFR 63
           ++D ++D++  LL  VP TL L   +L+ G  ++  +  +R+  + +  R   AY+ VFR
Sbjct: 2   NWDLMWDSVPTLLRGVPVTLQLVGLALLFGAGVAFAVALLRLYGNRVTERLMAAYVFVFR 61

Query: 64  GSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAV 123
           G+PLL+Q+FL+YYGMGQF ++R SFLW  LREP+ CA+L+L L T  YT+EI+RG +++V
Sbjct: 62  GTPLLVQIFLIYYGMGQFELVRSSFLWVYLREPFWCAILALTLNTGAYTSEILRGAILSV 121

Query: 124 PVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGV 183
           P GQIEA  + G+S   L RR++ P+A+RQ LPAY  E +L+VK+++LAS +T+ E+TG+
Sbjct: 122 PQGQIEAARACGMSRTLLFRRIMMPVAIRQMLPAYGNEVILMVKASSLASTITLLEITGI 181

Query: 184 AQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLRA 229
           A++II Q++   EVFI A  IYL LNF+  RL+   E R++ +LRA
Sbjct: 182 ARKIIAQSFAVFEVFIVAGSIYLLLNFIASRLIRYAEWRMTPYLRA 227


Lambda     K      H
   0.331    0.143    0.431 

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: 172
Number of extensions: 9
Number of successful extensions: 1
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: 250
Length of database: 229
Length adjustment: 23
Effective length of query: 227
Effective length of database: 206
Effective search space:    46762
Effective search space used:    46762
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 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