Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Korea:Ga0059261_4131 Length = 398 Score = 228 bits (582), Expect = 2e-64 Identities = 146/376 (38%), Positives = 209/376 (55%), Gaps = 18/376 (4%) Query: 81 GQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALTPGK 140 G+ ++DC+ G +GH +PV+V+A++ Q AK S P + LA+ L T Sbjct: 30 GEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISNMFEMPGQNALAERLT--TASF 87 Query: 141 LKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSATAKSTFR 197 FF NSGTE+VE A+K+A+ Y + RG + T I SGAFHG++ GA++A Sbjct: 88 ADTVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVIGFSGAFHGRTYGAMNAAGNPAHL 147 Query: 198 KPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAV 257 F LPGF H N A+ A+ + AAV++EP+QGEGG +L + Sbjct: 148 DGFGDRLPGFVHFAVDNWPALALAIADSA-----TAAVVVEPVQGEGGARAMTEPFLDKL 202 Query: 258 RKLCDEFGALMILDEVQTGMGRTGKMFACE-HENVQPDILCLAKALGGGVMPIGATIATE 316 R C G L+I DEVQTGMGRTGK+FA + + + PDI+ LAKALG G P+GA +AT Sbjct: 203 RAACTAHGVLLIYDEVQTGMGRTGKLFAHQWYPDATPDIMALAKALGSG-FPVGACLATA 261 Query: 317 EVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLARE 376 E S + P +H TT GGNPLA A A+A + + + A + L G +LA Sbjct: 262 EAASGMV--PGVHGTTAGGNPLAMAVAIAAFDEIAKPETLTHAREVAQHLRAGLDRLAAT 319 Query: 377 YPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIE 436 +P ++ E RGKG+L+ + V N + A+ QR+LVAG +N +R+ PPLTLT+ Sbjct: 320 HPGVISEIRGKGLLVGVRLVPNNRAFMAAAR--EQRLLVAGGGDNC--VRLLPPLTLTVA 375 Query: 437 QCELVIKAARKALAAM 452 + + ++ A AM Sbjct: 376 EADQILDRLDTACHAM 391 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: 437 Number of extensions: 21 Number of successful extensions: 7 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: 398 Length adjustment: 32 Effective length of query: 427 Effective length of database: 366 Effective search space: 156282 Effective search space used: 156282 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 Sep 17 2021. 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