GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Sinorhizobium meliloti 1021

Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase

Query= SwissProt::H3ZPU1
         (389 letters)



>FitnessBrowser__Smeli:SMc01578
          Length = 400

 Score =  251 bits (640), Expect = 3e-71
 Identities = 148/396 (37%), Positives = 235/396 (59%), Gaps = 22/396 (5%)

Query: 3   LSDRLEMVNPSEIRKLFDLAQGIEG----IISLGIGEPDFDTPEHIKEYAKEALDKGLTH 58
           L+D L  V PS    +   A+ ++     +I LG GEPDFDTP++IK+ A +A+D+G T 
Sbjct: 4   LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETK 63

Query: 59  YSPNIGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPS 118
           Y+P  GI ELREA+A+KFK+ N +D     Q ++  G  Q +       L   +EV+IP+
Sbjct: 64  YTPVSGIPELREAIAKKFKRENNLDYTA-AQTIVGTGGKQILFNAFMATLNPGDEVVIPA 122

Query: 119 PMFVSYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLT 178
           P +VSY   V L GG PV VPT +EN F+L  ++L++ +TPKT+  + N+P+NP+GA  +
Sbjct: 123 PYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYS 182

Query: 179 KKDLEEIADFAVEH-DLMILSDEVYEYFVYDGVKNYSIASLD-GMFERTITMNGFSKTFA 236
            ++L+ + D  ++H  + +L+D++YE+  Y   +  +   ++ G++ERT+TMNG SK +A
Sbjct: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242

Query: 237 MTGWRLGFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYER 296
           MTGWR+G+ A P  +++ M   Q    +   +  Q+AA +AL   + +  +   +  ++ 
Sbjct: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDF--IGRNKEIFQG 300

Query: 297 RRNLVWKRLNE-MGLPTVKPKGAFYIFPR----IKDTGLSSK------EFSELMIKEAKV 345
           RR+LV   LN+  G+    P+GAFY++P     I  T  S K      +F   +++   V
Sbjct: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360

Query: 346 VVVPGSAFGQAGEGYVRISYATAYEKLEEAMDRMEK 381
            VV GSAFG  G  + RISYAT+   LEEA  R+++
Sbjct: 361 AVVHGSAFG-LGPNF-RISYATSEALLEEACRRIQR 394


Lambda     K      H
   0.318    0.135    0.387 

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: 377
Number of extensions: 19
Number of successful extensions: 6
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: 389
Length of database: 400
Length adjustment: 31
Effective length of query: 358
Effective length of database: 369
Effective search space:   132102
Effective search space used:   132102
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: 50 (23.9 bits)

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