GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Pseudomonas simiae WCS417

Align tyrosine aminotransferase (EC 2.6.1.57) (characterized)
to candidate GFF3889 PS417_19910 aromatic amino acid aminotransferase

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



>FitnessBrowser__WCS417:GFF3889
          Length = 397

 Score =  684 bits (1765), Expect = 0.0
 Identities = 335/395 (84%), Positives = 359/395 (90%)

Query: 1   MHFDAIGRVPGDPILGLMEAYAQDSNPCKFDLGVGVYKDAQGLTPIPQSVKLAELRLVDR 60
           MHFDAIGRVPGDPILGLM+ YAQD+NP KFDLGVGVYKD QGLTPIP SVKLAE RLVD 
Sbjct: 1   MHFDAIGRVPGDPILGLMDLYAQDTNPNKFDLGVGVYKDDQGLTPIPHSVKLAEQRLVDT 60

Query: 61  QTTKTYIGGHGDPAFGKVINELVLGADSALIAEQRVGATQTPGGTGALRLSADFIAHCLP 120
           QTTKTYIGGHG+ AFGK+I+ELVLGADS LI E+R GATQTPGGTGALRLSADFIAH LP
Sbjct: 61  QTTKTYIGGHGNAAFGKLISELVLGADSTLIRERRAGATQTPGGTGALRLSADFIAHNLP 120

Query: 121 GRGIWLSNPTWPIHETIYATAGLKVSHYPYVGSDNRLDVEAMLATLNLIPKGDVVLLHAC 180
           GRG+WLSNPTWPIHETI+A AG+ VSHYPYVG+DNRLDV AMLATL+ +PKGDVVLLHAC
Sbjct: 121 GRGVWLSNPTWPIHETIFAKAGIPVSHYPYVGADNRLDVAAMLATLSTVPKGDVVLLHAC 180

Query: 181 CHNPTGFDLSHDDWRRVLEVVRSRELLPLIDFAYQGFGDGLEQDAWAVRLFAAELPELLI 240
           CHNPTGFDLS DDWR+VL++VR R+LLPLIDFAYQGFGDGLEQDAWAVRLFAAELPE+L+
Sbjct: 181 CHNPTGFDLSQDDWRQVLQIVRERQLLPLIDFAYQGFGDGLEQDAWAVRLFAAELPEVLV 240

Query: 241 TSSCSKNFGLYRDRTGALIVCAKDAEKLVDIRSQLANIARNLWSTPPDHGAAVVATILGD 300
           TSSCSKNFGLY DR GALIVCA DAEKL D+RSQLAN ARNLWSTPPDHGAAVVATILGD
Sbjct: 241 TSSCSKNFGLYSDRVGALIVCAADAEKLTDVRSQLANTARNLWSTPPDHGAAVVATILGD 300

Query: 301 PELKQLWADEVEAMRLRIAQLRSGLVEALEPHGLGERFAHIGVQRGMFSYTGLTPAQVKN 360
            ELK+ W+DEVEAMR RIA LRSGLVEAL PHGL  RFAHIG QRGMFSYTGL+  QVK 
Sbjct: 301 AELKKRWSDEVEAMRSRIAHLRSGLVEALAPHGLSARFAHIGAQRGMFSYTGLSAEQVKQ 360

Query: 361 LRDHHSVYMVSSGRANVAGIDATRLDLLAQAFADV 395
           LR+ HSVYMVSSGRANVAGIDATRL LLA+A ADV
Sbjct: 361 LREKHSVYMVSSGRANVAGIDATRLTLLAKAIADV 395


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: 623
Number of extensions: 12
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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