GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Bacteroides thetaiotaomicron VPI-5482

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 351943 BT2415 aspartate aminotransferase (NCBI ptt file)

Query= SwissProt::E9L7A5
         (479 letters)



>lcl|FitnessBrowser__Btheta:351943 BT2415 aspartate aminotransferase
           (NCBI ptt file)
          Length = 397

 Score =  391 bits (1004), Expect = e-113
 Identities = 205/400 (51%), Positives = 277/400 (69%), Gaps = 7/400 (1%)

Query: 76  LSPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHTR 135
           LS R+NS+ PS T+A++ ++  L   G+ VI L+ GEPDF+TP  I EA   AI +  +R
Sbjct: 4   LSDRLNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFSR 63

Query: 136 YTPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAP 195
           Y+P  G   LR+AI  KLK+ENGL YT  QI  +NGAKQS+  A+L + +PGDEV++PAP
Sbjct: 64  YSPVPGYPALRNAIVEKLKKENGLEYTAAQISCANGAKQSVCNAILVLVNPGDEVIVPAP 123

Query: 196 YWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPR 255
           YWVSYPEM ++A+ TPVI+   I +DF + PK LE+ +T K++ LILCSPSNPTGSVY +
Sbjct: 124 YWVSYPEMVKMAEGTPVIVSAGIEQDFKITPKQLEAAITPKTKALILCSPSNPTGSVYSK 183

Query: 256 KLLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAMT 315
           + L  +A ++A++P+++VI+DEIYEHI Y  A H S A  P M +RT+ VNG SKA+AMT
Sbjct: 184 EELAGLAAVLAKYPQVVVIADEIYEHINYIGA-HQSIAQFPEMKERTVIVNGVSKAYAMT 242

Query: 316 GWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAG-GELVATMVKSFRE 374
           GWR+G+IAGP+  + ACNK+Q Q+TSG  S+SQKAA AA    Y G  E V  M K+F  
Sbjct: 243 GWRIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAA----YVGTQEPVKEMQKAFER 298

Query: 375 RRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQV 434
           RRD +VK   E+ G +++ P+GAFYLF   S ++G + +G   I NS+ L  YLL+ A V
Sbjct: 299 RRDLIVKLAKEVPGFEVNVPQGAFYLFPKCSYFFG-KSNGERKIENSDDLAMYLLEDAHV 357

Query: 435 ALVPGDAFGDDTCIRISYAASLSTLQAAVERIKKALVTIK 474
           A V G +FG   CIR+SYA S   +  A+ RIK+AL  +K
Sbjct: 358 ACVGGTSFGAPECIRMSYATSDENIVEAIRRIKEALAKLK 397


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: 464
Number of extensions: 18
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: 397
Length adjustment: 32
Effective length of query: 447
Effective length of database: 365
Effective search space:   163155
Effective search space used:   163155
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.

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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 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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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