Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Koxy:BWI76_RS11670 Length = 406 Score = 198 bits (503), Expect = 3e-55 Identities = 135/375 (36%), Positives = 197/375 (52%), Gaps = 25/375 (6%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 G + L D QG+E+ID GG + +GH +P +V A+ Q K + LA Sbjct: 28 GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEPVLRLA 87 Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGA 187 K L T FFCNSG E+ EAALKLA+ Y R K +A AFHG++L Sbjct: 88 KQLIDATFADRV--FFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFT 145 Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247 +SA + + + F PL P +H + ++++ + ++ D+ AVI+EP+QGEGGV+ Sbjct: 146 VSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALID------DNTCAVIVEPMQGEGGVV 199 Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307 +L +R+LCD AL+I DEVQTG+GRTG+++A H V PD+L AKALGGG Sbjct: 200 PADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGG-F 258 Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367 PIGA +A+E SV+ H TT+GGNPLACA A + + + +Q+ Sbjct: 259 PIGALLASERCASVM--TVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFC 316 Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG-----YNFASEMFRQRVLVAGTLNNA 422 + + Y L +E RG G+L+ D G N A+E +L+AG A Sbjct: 317 ERLNAINARY-GLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEE-GLMILIAG----A 370 Query: 423 KTIRIEPPLTLTIEQ 437 +R P L ++ ++ Sbjct: 371 NVVRFAPALIISEDE 385 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: 417 Number of extensions: 20 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 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