Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__psRCH2:GFF2666 Length = 406 Score = 208 bits (529), Expect = 3e-58 Identities = 137/383 (35%), Positives = 203/383 (53%), Gaps = 25/383 (6%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 D G+E +D GG + +GH +P +V+A+ Q K S + LAK L A T Sbjct: 38 DQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHISNIYTNEPALRLAKKLVAAT 97 Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQ----SPRGKFTFIATSGAFHGKSLGALSATAK 193 +FFCNSG E+ EAA KLA+ Y P+ KF I+ +FHG++L ++ + Sbjct: 98 FADR--AFFCNSGAEANEAAFKLARRYAHDVYGPQ-KFEIISALNSFHGRTLFTVTVGGQ 154 Query: 194 STFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGY 253 S + F P + G HVP+ ++EA++ A++ D AV+LEPIQGE G++ Y Sbjct: 155 SKYSDGFGPKIEGITHVPYNDLEALKAAIS------DKTCAVVLEPIQGESGILPGEQAY 208 Query: 254 LTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATI 313 L R+LC+E AL+I DEVQTGMGRTG++FA H + PDIL AK+LGGG PIGA + Sbjct: 209 LEGARQLCNEHNALLIFDEVQTGMGRTGELFAYMHYGITPDILTNAKSLGGG-FPIGAML 267 Query: 314 ATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQL 373 T E+ + L + H TT+GGNPLACA A A ++++ + + K + Q+ Sbjct: 268 TTNEIAAHL--SVGTHGTTYGGNPLACAVAEAVVDIVNTPEVLEGVKAKHERFKARLTQI 325 Query: 374 AREYPDLVQEARGKGMLMAIEFVDNEIG----YNFASEMFRQRVLVAGTLNNAKTIRIEP 429 Y + RG+G+L+ D G + A+E VL AG +R+ P Sbjct: 326 GERY-GVFSLVRGRGLLIGCVLSDAWKGKAGAFCAAAEKEALMVLQAG----PDVVRLAP 380 Query: 430 PLTLTIEQCELVIKAARKALAAM 452 L + + + +A+AA+ Sbjct: 381 SLVIDQADIDEGLDRLERAVAAL 403 Lambda K H 0.320 0.135 0.393 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: 383 Number of extensions: 16 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