GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1695 in Azospirillum brasilense Sp245

Align ABC transporter permease (characterized, see rationale)
to candidate AZOBR_RS08235 AZOBR_RS08235 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:A0A165KC95
         (309 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS08235 AZOBR_RS08235
           branched-chain amino acid transporter permease subunit
           LivH
          Length = 301

 Score =  256 bits (655), Expect = 4e-73
 Identities = 141/307 (45%), Positives = 199/307 (64%), Gaps = 18/307 (5%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           M+  LQQ+INGL LG++Y LIA+GYTMVYGII +INFAHGE+ MIGA      + ++   
Sbjct: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAF-----VALITFL 55

Query: 61  MPGAPG--WV--ILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQ 116
             G+ G  WV   LL+  + + +  A   + +E++AYRPLRSSPRLAPLI+AIGMSI LQ
Sbjct: 56  AIGSLGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQ 115

Query: 117 TLAMIIWKPNYKPYPTMLPSSPFEIGGAF-ITPTQILILGVTAVALASLVYLVNHTNLGR 175
               I+     KP   +LP +   + GA  ++  ++  + +T   +     L+  T+LGR
Sbjct: 116 NYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGR 175

Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235
           A RA  ++ ++A L+GV  D VIS TF++GA LAA+AG+M    YG     +GFL G+KA
Sbjct: 176 AQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKA 235

Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295
           FTAAV GGIG+L GA++GG+++GLIEA  SGY        +GS + D+  F +L+++L  
Sbjct: 236 FTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGY--------MGSEWKDVATFTILVLVLIF 287

Query: 296 RPSGLLG 302
           RP+GLLG
Sbjct: 288 RPTGLLG 294


Lambda     K      H
   0.327    0.142    0.419 

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: 297
Number of extensions: 15
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: 309
Length of database: 301
Length adjustment: 27
Effective length of query: 282
Effective length of database: 274
Effective search space:    77268
Effective search space used:    77268
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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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