GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase 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)



>FitnessBrowser__Btheta:351943
          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 (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