GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Sinorhizobium fredii NGR234

Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate YP_002822392.1 NGR_b01730 aspartate aminotransferase

Query= SwissProt::A3PMF8
         (400 letters)



>NCBI__GCF_000018545.1:YP_002822392.1
          Length = 400

 Score =  445 bits (1144), Expect = e-129
 Identities = 215/399 (53%), Positives = 277/399 (69%)

Query: 1   MAFLSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAG 60
           M  L+D L  V  S + A+T +AR+LA+ G DV+ L +GEPDF TP +   AA  A  AG
Sbjct: 1   MPTLADRLKNVSVSASAAMTQRARDLASRGVDVVSLSSGEPDFPTPSHAIEAAHAAALAG 60

Query: 61  RTKYTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVII 120
            TKY  +DG P LK AI  KF+R+N L Y P Q+ V  GGKQ+++NA++AT NPGDEV+I
Sbjct: 61  DTKYPPLDGTPALKAAIARKFKRDNNLDYEPGQILVSGGGKQVIFNAVLATCNPGDEVVI 120

Query: 121 PAPYWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAA 180
           P+P W+SY D+V  AGG PV VA   E GFKL PE LEAAITPRTKW + N P+NPTGAA
Sbjct: 121 PSPAWISYADIVRFAGGVPVPVACSHENGFKLRPEDLEAAITPRTKWLLLNFPNNPTGAA 180

Query: 181 YTRAELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKA 240
            +R E+AA+ EV++RH  VWIM+DDMYEHLV+DDF+F T A++EP LYDR LT NG SKA
Sbjct: 181 CSRQEMAAIAEVMLRHADVWIMTDDMYEHLVYDDFEFCTIAEVEPRLYDRVLTVNGASKA 240

Query: 241 YCMTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQR 300
           Y MTGWR+G+  GP  LI A+  +  Q++    +I Q A +  L GPQ+ L      +++
Sbjct: 241 YAMTGWRLGFCGGPKALISAISNVNGQNSGGTSTITQAAVVAVLDGPQDLLKERAAIYRK 300

Query: 301 RRDLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGV 360
           RRD V+  L+   G+TC  PEGAFY++P I+G IGKT+  G +I  D  F  AL++E  V
Sbjct: 301 RRDFVLENLDGIDGLTCHKPEGAFYLFPSIAGLIGKTTKAGRRIETDTDFVMALIDEQHV 360

Query: 361 AVVFGAAFGLSPNFRISYATADEVLREACARIQAFCAGL 399
           A+V GAA+G+SP FRISYAT+ E L + CARI  FC+ L
Sbjct: 361 AIVQGAAYGMSPFFRISYATSVEKLADGCARIAEFCSNL 399


Lambda     K      H
   0.318    0.134    0.399 

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: 499
Number of extensions: 19
Number of successful extensions: 1
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 10 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