Align Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family
Query= curated2:B7LZM2 (459 letters) >FitnessBrowser__psRCH2:GFF2666 Length = 406 Score = 207 bits (527), Expect = 5e-58 Identities = 139/390 (35%), Positives = 207/390 (53%), Gaps = 26/390 (6%) Query: 72 GLNTLV-DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 GL + V D G+E +D GG + +GH +P +V+A+ Q K S + LA Sbjct: 31 GLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHISNIYTNEPALRLA 90 Query: 131 KTVAALTPGKLKYSFFCNSGTESVEAALKLAKAYQ----SPRGKFTFIATSGAFHGKSLG 186 K + A T +FFCNSG E+ EAA KLA+ Y P+ KF I+ +FHG++L Sbjct: 91 KKLVAATFADR--AFFCNSGAEANEAAFKLARRYAHDVYGPQ-KFEIISALNSFHGRTLF 147 Query: 187 ALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGV 246 ++ +S + F P + G HVP+ ++EA++ A++ D AV+LEPIQGE G+ Sbjct: 148 TVTVGGQSKYSDGFGPKIEGITHVPYNDLEALKAAIS------DKTCAVVLEPIQGESGI 201 Query: 247 ILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGV 306 + YL R+LC+E AL+I DEVQTGMGRTG++FA H + PDIL AK+LGGG Sbjct: 202 LPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFAYMHYGITPDILTNAKSLGGG- 260 Query: 307 MPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDML 366 PIGA + T E+ + L + H TT+GGNPLACA A A ++++ + + K + Sbjct: 261 FPIGAMLTTNEIAAHL--SVGTHGTTYGGNPLACAVAEAVVDIVNTPEVLEGVKAKHERF 318 Query: 367 LDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG----YNFASEMFRQRVLVAGTLNNA 422 Q+ Y + RG+G+L+ D G + A+E VL AG Sbjct: 319 KARLTQIGERY-GVFSLVRGRGLLIGCVLSDAWKGKAGAFCAAAEKEALMVLQAG----P 373 Query: 423 KTIRIEPPLTLTIEQCELVIKAAHKALAAM 452 +R+ P L + + + +A+AA+ Sbjct: 374 DVVRLAPSLVIDQADIDEGLDRLERAVAAL 403 Lambda K H 0.320 0.136 0.395 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: 396 Number of extensions: 17 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: 459 Length of database: 406 Length adjustment: 32 Effective length of query: 427 Effective length of database: 374 Effective search space: 159698 Effective search space used: 159698 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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:
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