GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Dechlorosoma suillum PS

Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase

Query= SwissProt::E9L7A5
         (479 letters)



>FitnessBrowser__PS:Dsui_0132
          Length = 385

 Score =  184 bits (466), Expect = 6e-51
 Identities = 126/400 (31%), Positives = 197/400 (49%), Gaps = 26/400 (6%)

Query: 77  SPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHTRY 136
           +PR+  + P   + +  +A  L   G  +I +  GEPDF TP PI+ A    +++G   Y
Sbjct: 5   APRLADIAPFHVMELLGRARELEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFY 64

Query: 137 TPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPY 196
           TP  G  ELR AIS   ++  G++    +I ++ GA  ++  A+  + +PG E L+  P 
Sbjct: 65  TPALGLPELREAISGFYRQRYGIAVPASRIAITAGASGALTLALACLAAPGSEWLLTDPG 124

Query: 197 WVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRK 256
           +       R  +  PV +P   + +F      LE    E++   +  SP+NPTG++    
Sbjct: 125 YPCNRHFVRAFEGVPVSIPVGAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAA 184

Query: 257 LLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAMTG 316
            L  IA+ V +    L+I DEIY  + Y     T+ A+     D    V  FSK F MTG
Sbjct: 185 ELADIADFVRQRQGQLII-DEIYHGLTYNGDAPTALAA----GDNIFVVQSFSKYFQMTG 239

Query: 317 WRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVK---SFR 373
           WRLG++  P+ F+    K+       AS+ +Q AA+AA        E +A + +    F+
Sbjct: 240 WRLGWLVIPEPFVRDVEKLAQNLFISASTPAQHAALAAF-----QPETIALLEQRRAEFK 294

Query: 374 ERRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQ 433
            RRDYL  +   I     ++P GAFYL+ D S+   +  D FG         R LL++A 
Sbjct: 295 ARRDYLAPALEAIGFRITAQPEGAFYLYADCST---LTDDSFG-------FARRLLEEAG 344

Query: 434 VALVPGDAFGD---DTCIRISYAASLSTLQAAVERIKKAL 470
           VA+ PG  FG+    + +R +Y  + + L   VERI++ L
Sbjct: 345 VAITPGIDFGNHGASSHVRFAYTNAQARLAEGVERIRQLL 384


Lambda     K      H
   0.317    0.132    0.375 

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: 402
Number of extensions: 22
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: 479
Length of database: 385
Length adjustment: 32
Effective length of query: 447
Effective length of database: 353
Effective search space:   157791
Effective search space used:   157791
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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