GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Azospirillum brasilense Sp245

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AZOBR_RS12970 AZOBR_RS12970 aspartate aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS12970 AZOBR_RS12970 aspartate
           aminotransferase
          Length = 401

 Score =  584 bits (1506), Expect = e-171
 Identities = 288/396 (72%), Positives = 319/396 (80%)

Query: 1   MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60
           M+ +A  LSR+KPS TIAV+QKAREL A GRDVIGLGAGEPDFDTPDNIK AAI AI  G
Sbjct: 1   MSIIASRLSRIKPSPTIAVTQKARELAAAGRDVIGLGAGEPDFDTPDNIKDAAIKAIQAG 60

Query: 61  ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120
           +TKYT V G P L++AI  KF+REN L Y   Q  VG GGKQ+L+NA MATL PGDEV+I
Sbjct: 61  DTKYTAVDGTPALKKAICAKFERENGLKYAPDQITVGVGGKQVLYNALMATLTPGDEVII 120

Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180
           PAPYWVSYP+MV L  GTPVFV    E  FKL+  DL++AITPKTKW + NSPSNPSGAA
Sbjct: 121 PAPYWVSYPDMVELAEGTPVFVSCPAEQGFKLQPADLEKAITPKTKWLILNSPSNPSGAA 180

Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240
           Y+ +E+KALTDVL+KHP VWV+TDDMYEHL Y    F TP +VEP LY+RTLT+NGVSK+
Sbjct: 181 YTRDEMKALTDVLVKHPQVWVMTDDMYEHLLYDGIEFVTPAQVEPALYDRTLTVNGVSKS 240

Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300
           YAMTGWRIGYA GP  LIKAM +IQ Q TS   SIAQ AAVEALNGPQDFI     +F  
Sbjct: 241 YAMTGWRIGYAGGPKALIKAMGVIQSQSTSNPTSIAQAAAVEALNGPQDFIAERAAVFAQ 300

Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360
           RRDLVVSMLNQAKGISCP PEGAFYVYPSCAG IGKT P GKVIETDEDFV+ LLE+EGV
Sbjct: 301 RRDLVVSMLNQAKGISCPKPEGAFYVYPSCAGTIGKTTPDGKVIETDEDFVTYLLESEGV 360

Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFC 396
           AVV GSAFGL P+FRISYATS   LEEAC+RIQR C
Sbjct: 361 AVVQGSAFGLAPHFRISYATSTEALEEACKRIQRAC 396


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: 598
Number of extensions: 16
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: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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