GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Pseudomonas fluorescens FW300-N2C3

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AO356_25355 AO356_25355 aspartate aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25355 AO356_25355
           aspartate aminotransferase
          Length = 404

 Score =  466 bits (1200), Expect = e-136
 Identities = 225/393 (57%), Positives = 292/393 (74%)

Query: 8   LSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPV 67
           L+R + SAT  +  +  E +A+G  +I L AGEPDFDTP +I++AAI+AI +G T+YT V
Sbjct: 12  LARAQSSATYRIMDRVAERRAQGAKIISLCAGEPDFDTPKHIREAAIEAIGQGHTRYTQV 71

Query: 68  SGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVS 127
           +G+  LREA+A KF++EN LD T   T+V  GGKQ+++NA  ATL+ GD+V++PAPYWVS
Sbjct: 72  AGVRSLREAVAAKFRQENGLDVTWQDTLVCNGGKQVIYNALAATLDEGDQVIVPAPYWVS 131

Query: 128 YPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELK 187
           YPEMV LCGG    V    ++ FKL    LD AITP+T+W + NSPSNP+GA YS EEL+
Sbjct: 132 YPEMVQLCGGESRIVTCDADSGFKLTPAALDAAITPQTRWLILNSPSNPTGAVYSREELQ 191

Query: 188 ALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWR 247
           AL DVL+ HPHV +L DD+YEHL + D  F T  +VEP L  RTLTMNGVSKAYAMTGWR
Sbjct: 192 ALADVLLAHPHVLILADDIYEHLIFDDQVFYTLAQVEPRLASRTLTMNGVSKAYAMTGWR 251

Query: 248 IGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVS 307
           IG+A GP  L++AM+ +QGQQTSGA+SI+Q AA+ AL+GP+DFI  ++ +FQ RRDL+V+
Sbjct: 252 IGFATGPRWLLEAMEKLQGQQTSGASSISQQAALAALDGPKDFIRESRAVFQRRRDLMVA 311

Query: 308 MLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSA 367
           +LN   G++C +P GAFY + SCAGLIG+T+  G+V+ TDED    LL+   VAVVHGSA
Sbjct: 312 LLNATPGLACASPGGAFYAFASCAGLIGRTSSGGRVLHTDEDVAHALLDEADVAVVHGSA 371

Query: 368 FGLGPNFRISYATSEALLEEACRRIQRFCAACR 400
           FGLGP  RI+YA  +A L +AC  I+ FC A R
Sbjct: 372 FGLGPYIRIAYALDDASLRQACEAIRGFCDALR 404


Lambda     K      H
   0.318    0.134    0.402 

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: 477
Number of extensions: 17
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: 404
Length adjustment: 31
Effective length of query: 369
Effective length of database: 373
Effective search space:   137637
Effective search space used:   137637
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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