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 352902 BT3375 aspartate aminotransferase (NCBI ptt file)

Query= SwissProt::E9L7A5
         (479 letters)



>FitnessBrowser__Btheta:352902
          Length = 386

 Score =  232 bits (591), Expect = 2e-65
 Identities = 138/398 (34%), Positives = 219/398 (55%), Gaps = 21/398 (5%)

Query: 74  ISLSPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGH 133
           I LS   NS+ PS    +T +   L Q    VI    G+PD      I EAG  AI EG 
Sbjct: 2   IQLSEITNSISPS----LTRRLFNLAQKYDNVIDFTLGDPDIHPHDKIKEAGCKAILEGR 57

Query: 134 TRYTPNAGTMELRSAISHKLKEENGLSYTP-DQILVSNGAKQSIIQAVLAVCSPGDEVLI 192
           TRY+PNAG +ELR  IS + K +  + Y P ++I+V+ G  + +   +LA+ + GDEV+I
Sbjct: 58  TRYSPNAGLLELREIISSRYKLQYNIEYNPTNEIMVTVGGMEGLYLTLLAILNRGDEVII 117

Query: 193 PAPYWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSV 252
           PAPYW++Y +M  +    P+I     + D  +  + +   +T K++ +IL +PSNP+G +
Sbjct: 118 PAPYWINYVQMVCMCSGEPIITAPVSTNDLSISIENIRKAITPKTKAIILNTPSNPSGRI 177

Query: 253 YPRKLLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAF 312
                ++QIA+I   +  L+VI+DE+Y+ ++Y  A   S  +   M +RT+ +N  SK F
Sbjct: 178 ISDDSIQQIAQIAIEND-LIVITDEVYKTLLYDNAHFKSIVTCDKMKERTVVINSLSKEF 236

Query: 313 AMTGWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSF 372
            MTGWRLGYIA P   I+     Q    + A   SQ AA+ AL       +  A M++ F
Sbjct: 237 CMTGWRLGYIAAPSELISVMTMFQENIAACAPLPSQYAAIEAL---RNSEKYSAGMIEEF 293

Query: 373 RERRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKA 432
             RR+ L++   +I+ + +  P+G FY  +++ S  G++         SE     LL+K 
Sbjct: 294 TLRRNVLLEEVAKIKTITVDAPQGTFYAMLNIKS-TGLK---------SEEFAYALLEKE 343

Query: 433 QVALVPGDAFGD--DTCIRISYAASLSTLQAAVERIKK 468
           QVA+VPG  +GD  +  IRI++   +  ++  ++R+K+
Sbjct: 344 QVAVVPGITYGDCCEDFIRIAFTLDIYKIKEGIQRLKR 381


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: 399
Number of extensions: 21
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: 479
Length of database: 386
Length adjustment: 32
Effective length of query: 447
Effective length of database: 354
Effective search space:   158238
Effective search space used:   158238
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