GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Pseudomonas fluorescens FW300-N2E3

Align tyrosine aminotransferase (EC 2.6.1.57) (characterized)
to candidate AO353_18575 AO353_18575 aromatic amino acid aminotransferase

Query= reanno::pseudo3_N2E3:AO353_18575
         (397 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_18575 AO353_18575 aromatic
           amino acid aminotransferase
          Length = 397

 Score =  803 bits (2075), Expect = 0.0
 Identities = 397/397 (100%), Positives = 397/397 (100%)

Query: 1   MHFDAIGRVPGDPILGLMEAYAQDSNPCKFDLGVGVYKDAQGLTPIPQSVKLAELRLVDR 60
           MHFDAIGRVPGDPILGLMEAYAQDSNPCKFDLGVGVYKDAQGLTPIPQSVKLAELRLVDR
Sbjct: 1   MHFDAIGRVPGDPILGLMEAYAQDSNPCKFDLGVGVYKDAQGLTPIPQSVKLAELRLVDR 60

Query: 61  QTTKTYIGGHGDPAFGKVINELVLGADSALIAEQRVGATQTPGGTGALRLSADFIAHCLP 120
           QTTKTYIGGHGDPAFGKVINELVLGADSALIAEQRVGATQTPGGTGALRLSADFIAHCLP
Sbjct: 61  QTTKTYIGGHGDPAFGKVINELVLGADSALIAEQRVGATQTPGGTGALRLSADFIAHCLP 120

Query: 121 GRGIWLSNPTWPIHETIYATAGLKVSHYPYVGSDNRLDVEAMLATLNLIPKGDVVLLHAC 180
           GRGIWLSNPTWPIHETIYATAGLKVSHYPYVGSDNRLDVEAMLATLNLIPKGDVVLLHAC
Sbjct: 121 GRGIWLSNPTWPIHETIYATAGLKVSHYPYVGSDNRLDVEAMLATLNLIPKGDVVLLHAC 180

Query: 181 CHNPTGFDLSHDDWRRVLEVVRSRELLPLIDFAYQGFGDGLEQDAWAVRLFAAELPELLI 240
           CHNPTGFDLSHDDWRRVLEVVRSRELLPLIDFAYQGFGDGLEQDAWAVRLFAAELPELLI
Sbjct: 181 CHNPTGFDLSHDDWRRVLEVVRSRELLPLIDFAYQGFGDGLEQDAWAVRLFAAELPELLI 240

Query: 241 TSSCSKNFGLYRDRTGALIVCAKDAEKLVDIRSQLANIARNLWSTPPDHGAAVVATILGD 300
           TSSCSKNFGLYRDRTGALIVCAKDAEKLVDIRSQLANIARNLWSTPPDHGAAVVATILGD
Sbjct: 241 TSSCSKNFGLYRDRTGALIVCAKDAEKLVDIRSQLANIARNLWSTPPDHGAAVVATILGD 300

Query: 301 PELKQLWADEVEAMRLRIAQLRSGLVEALEPHGLGERFAHIGVQRGMFSYTGLTPAQVKN 360
           PELKQLWADEVEAMRLRIAQLRSGLVEALEPHGLGERFAHIGVQRGMFSYTGLTPAQVKN
Sbjct: 301 PELKQLWADEVEAMRLRIAQLRSGLVEALEPHGLGERFAHIGVQRGMFSYTGLTPAQVKN 360

Query: 361 LRDHHSVYMVSSGRANVAGIDATRLDLLAQAFADVCK 397
           LRDHHSVYMVSSGRANVAGIDATRLDLLAQAFADVCK
Sbjct: 361 LRDHHSVYMVSSGRANVAGIDATRLDLLAQAFADVCK 397


Lambda     K      H
   0.321    0.138    0.423 

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: 744
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 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, the preprint 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