GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braD in Azospirillum brasilense Sp245

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate AZOBR_RS32415 AZOBR_RS32415 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS32415 AZOBR_RS32415
           branched-chain amino acid ABC transporter permease
          Length = 305

 Score =  191 bits (485), Expect = 2e-53
 Identities = 101/304 (33%), Positives = 177/304 (58%), Gaps = 21/304 (6%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +LQQ++NGL++G  YAL+AIG+T+++G++ ++NFAHGEVY IG+++  + IT +A   L 
Sbjct: 7   FLQQVINGLSIGCVYALMAIGFTLIFGVLNVVNFAHGEVYTIGAFVGLMVITAMAPPLLA 66

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRG----------GNRLIPLISAIGMSIF 116
            VPL++         V +  G  +ER+A+RP R             R   L+S++ +SI 
Sbjct: 67  VVPLVLA--------VGAVSGVGLERIAFRPFRRFTDEASQKSRAMREATLLSSLAVSIM 118

Query: 117 LQNAVMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISR 176
            +  +M       + IP+   G  +    ++  ++++   ++IF  + +++  L   + R
Sbjct: 119 TREIMMHIFGGDMQGIPS---GYLLQQPVAIGPIMVASGSLVIFATSAVMLGALQFLLYR 175

Query: 177 SRLGRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFL 236
           ++ G   RA + +      +GIN++  I  TF +G+ L A A +L+G+  G I+P +GF 
Sbjct: 176 TQTGLGIRAVSNNQLGARYVGINTDRTIVTTFAVGSMLGATAGILVGLYDGAISPHMGFA 235

Query: 237 AGIKAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPT 296
            G+KAF A V+GG+ SIPGA+   LLLGV+E+   +     +KD++ + LL++ L+F P 
Sbjct: 236 PGVKAFVAMVMGGLSSIPGAVACALLLGVSESIATEFLSSGWKDLITYSLLVITLVFFPQ 295

Query: 297 GILG 300
           G+ G
Sbjct: 296 GLFG 299


Lambda     K      H
   0.328    0.145    0.413 

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: 273
Number of extensions: 16
Number of successful extensions: 3
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: 307
Length of database: 305
Length adjustment: 27
Effective length of query: 280
Effective length of database: 278
Effective search space:    77840
Effective search space used:    77840
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: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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