Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__SB2B:6938908 Length = 404 Score = 195 bits (495), Expect = 3e-54 Identities = 134/385 (34%), Positives = 202/385 (52%), Gaps = 25/385 (6%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQ-PLHSQELLDPLRAMLAKTLAAL 136 D QG E++D GG + +GH +P +V A++ Q K L + +P A+ K + A Sbjct: 37 DQQGTEYVDFAGGIAVNCLGHCHPALVGALKEQGEKLWHLSNTMTNEPALALATKLVEAT 96 Query: 137 TPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGALSATAK 193 ++ +F NSG E+ EAALKLA+ Y + K IA AFHG++ +S + Sbjct: 97 FADRV---YFANSGAEANEAALKLARRYAIEKFGEHKVEVIAFDKAFHGRTFFTVSVGGQ 153 Query: 194 STFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGY 253 + + F P H+PF +I A+ A++ D+ A++LEP+QGEGG+I P + Sbjct: 154 AAYSDGFGPKPAAITHLPFNDIAALEAAVS------DNTCAIMLEPLQGEGGIINGDPEF 207 Query: 254 LTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATI 313 L AVR+L D+ AL+I DEVQTG+GRTG ++A + PDIL AKALGGG PI A + Sbjct: 208 LRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPDILTTAKALGGG-FPIAAML 266 Query: 314 ATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQL 373 T ++ S L H +T+GGNPLACA A ++V+ + + + + DG Q+ Sbjct: 267 TTADIASHL--KVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLDGVKHREQLFRDGLAQI 324 Query: 374 AREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN---NAKTIRIEPP 430 +Y + E RGKG+L+ + G S F + G L A +R P Sbjct: 325 NEKY-HVFSEIRGKGLLLGAVLNEQFAG---RSRDFLNASVAEGLLTLMAGANVVRFTP- 379 Query: 431 LTLTIEQCELVIKAARKALAAMRVS 455 +L I + ++V AR A +V+ Sbjct: 380 -SLVIPEADIVEGLARFERAVAKVA 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: 381 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: 404 Length adjustment: 32 Effective length of query: 427 Effective length of database: 372 Effective search space: 158844 Effective search space used: 158844 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