GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Dechlorosoma suillum PS

Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase

Query= curated2:O67781
         (394 letters)



>FitnessBrowser__PS:Dsui_0132
          Length = 385

 Score =  211 bits (537), Expect = 3e-59
 Identities = 135/390 (34%), Positives = 202/390 (51%), Gaps = 14/390 (3%)

Query: 6   ASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTKY 65
           A R++ + P   + +  +A+EL A+G D+I    GEPDF TP+ I  A    L++G+  Y
Sbjct: 5   APRLADIAPFHVMELLGRARELEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFY 64

Query: 66  APSAGIPELREAIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPY 125
            P+ G+PELREAI+    +   +    S I ++AGA   L L    +   G E LL  P 
Sbjct: 65  TPALGLPELREAISGFYRQRYGIAVPASRIAITAGASGALTLALACLAAPGSEWLLTDPG 124

Query: 126 WVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEE 185
           +      +R F GVPV +P+     FQ +  D+++   ERT   +  SP NPTG + +  
Sbjct: 125 YPCNRHFVRAFEGVPVSIPVGAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAA 184

Query: 186 ELKKIAEFCVERGIFIISDECYEYFVY-GDAKFVSPASFSDEVKNITFTVNAFSKSYSMT 244
           EL  IA+F  +R   +I DE Y    Y GDA     A   D +    F V +FSK + MT
Sbjct: 185 ELADIADFVRQRQGQLIIDEIYHGLTYNGDAPTALAA--GDNI----FVVQSFSKYFQMT 238

Query: 245 GWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRR 304
           GWR+G++  PE + + +  L      + +T AQ+ AL A + P++   + + R  F+ RR
Sbjct: 239 GWRLGWLVIPEPFVRDVEKLAQNLFISASTPAQHAALAAFQ-PETIALLEQRRAEFKARR 297

Query: 305 DTAVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAF- 363
           D     L  I      +PEGAFY++ D S   +   G    +  LLE+A VA+ PG  F 
Sbjct: 298 DYLAPALEAIGFRITAQPEGAFYLYADCSTLTDDSFG---FARRLLEEAGVAITPGIDFG 354

Query: 364 --GAPGFLRLSYALSEERLVEGIRRIKKAL 391
             GA   +R +Y  ++ RL EG+ RI++ L
Sbjct: 355 NHGASSHVRFAYTNAQARLAEGVERIRQLL 384


Lambda     K      H
   0.317    0.135    0.383 

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: 378
Number of extensions: 19
Number of successful extensions: 5
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: 394
Length of database: 385
Length adjustment: 30
Effective length of query: 364
Effective length of database: 355
Effective search space:   129220
Effective search space used:   129220
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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