Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 226 bits (576), Expect = 1e-63 Identities = 137/380 (36%), Positives = 209/380 (55%), Gaps = 13/380 (3%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 DTQG+ ++D + G +GH +P +V A+ +Q+ K S P + LA L A + Sbjct: 48 DTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHVSNLYYIPEQGQLAAWLTANS 107 Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSP--RGKFTFIATSGA-FHGKSLGALSATAKS 194 FFCNSG E+ EAA+KLA+ + + + I T+ A FHG++L A++AT + Sbjct: 108 CADRV--FFCNSGAEANEAAIKLARKHGNTVLEAENPIILTAQASFHGRTLAAVTATGQP 165 Query: 195 TFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYL 254 + K F PL+ GFR+VP+ ++ A+ L E G+ VAA++LEP+QGEGGV Y Sbjct: 166 KYHKGFQPLVQGFRYVPYNDLAALEATLAELDAAGETVAAILLEPLQGEGGVNPGDRAYF 225 Query: 255 TAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIA 314 AVR+LCD+ L+ILDEVQ GMGR+G+++ E+ ++PD +AK LGGGV PIGA + Sbjct: 226 QAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYENLGIEPDAFTVAKGLGGGV-PIGALLV 284 Query: 315 TEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLA 374 + H +TFGGNPLAC A LA V+ L A + +G+ L G ++L Sbjct: 285 KASCNILQAGE---HASTFGGNPLACRAGLAIAQVMERDQLLANVQARGEQLRAGLQELV 341 Query: 375 REYPDLVQEARGKGML--MAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLT 432 YP+L+ RG G++ + + N Q +L+ A+ +R PPL Sbjct: 342 DRYPNLLAGVRGWGLINGLVLRNDPNVTPIALVKAAIEQGLLLVPA--GAEVVRFVPPLI 399 Query: 433 LTIEQCELVIKAARKALAAM 452 ++ + + + +AL A+ Sbjct: 400 VSAAEIDEALAMTERALLAI 419 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: 433 Number of extensions: 22 Number of successful extensions: 4 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: 422 Length adjustment: 32 Effective length of query: 427 Effective length of database: 390 Effective search space: 166530 Effective search space used: 166530 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