Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Pedo557:CA265_RS15205 Length = 378 Score = 257 bits (657), Expect = 4e-73 Identities = 151/376 (40%), Positives = 218/376 (57%), Gaps = 26/376 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQ---ELLDPLRAMLAKT 132 + D Q ++ ID + G G+ NVGH +P VV A+Q Q A+ +H E + + AK Sbjct: 12 IYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQ-AETYMHLMVYGEYVQTPQVNFAKA 70 Query: 133 LAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192 LA + P L ++F NSGTE+VE A+KLAK Y +G FIA A+HG + GA S Sbjct: 71 LADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKG---FIACKNAYHGSTQGAESLME 127 Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252 + + P LP + N+ + NE +AAV +EPIQGE G+ + Sbjct: 128 SDFYSSGYGPFLPHVSFIEHNNLADLEKITNE-------IAAVFIEPIQGEAGIRVSDLS 180 Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312 Y+ A+R C E G L+I DE+Q+G GR+GKMFA EH NV PD+L LAK +GGG MPIGA Sbjct: 181 YMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAKGIGGG-MPIGAF 239 Query: 313 IATEEVFSVLFDNPFL-HTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 I++ E+ SVL P L H TTFGG+P+ CAA LAT+ L++ ++ + E+KG + F+ Sbjct: 240 ISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEVEEKGQL----FK 295 Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431 QL + ++E RGKG+++A+EF + EI VL L+ + ++RI PPL Sbjct: 296 QLLQH--PAIKEIRGKGLMLAVEFENFEINKKIIDACILDGVLSDWFLHCSNSMRIAPPL 353 Query: 432 TLTIEQ----CELVIK 443 +T E+ C +++K Sbjct: 354 IITKEEIAEACTIILK 369 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: 419 Number of extensions: 31 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: 378 Length adjustment: 31 Effective length of query: 428 Effective length of database: 347 Effective search space: 148516 Effective search space used: 148516 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: 50 (23.9 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