Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 186 bits (472), Expect = 1e-51 Identities = 125/372 (33%), Positives = 193/372 (51%), Gaps = 20/372 (5%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 D Q+++D GG + ++GH NP V+ + +QL K +S + PL+ LA+ L ++ Sbjct: 24 DANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYSNSVKIPLQVQLAEKLGEVS 83 Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFR 197 K F CNSG E+ E ALKLA Y G+ IA +GAFHG++ A++ T Sbjct: 84 GKKDFQLFLCNSGAEANENALKLASFYN---GRKKVIAFTGAFHGRTSLAVAVTDNPKIV 140 Query: 198 KPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAV 257 P + +PF N A+ K G++++AVI+E IQG GG+ +L + Sbjct: 141 AP-VNQTENVIFLPFNNEIALEETF---KAQGNEISAVIIEGIQGVGGIKEASKSFLQKI 196 Query: 258 RKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEE 317 R LCDE+ A+ I D VQ G GRTG ++ ++ V+ D+ +AK +G G G +IA++ Sbjct: 197 RSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKGMGNGFPVAGISIASK- 255 Query: 318 VFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREY 377 F TTFGGN LACAAALA + V+ + NL AE+ G+ L+ ++ Sbjct: 256 -FKPWHGE---LGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGNYLIAELKKF---- 307 Query: 378 PDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQ 437 + V E RG+G+++ IE + E+ + +F + N IR+ P L LT Sbjct: 308 -EQVVEVRGRGLMIGIE-LPAELAHVKKELLFTHHIFTGEAKPN--VIRLLPALNLTKAH 363 Query: 438 CELVIKAARKAL 449 + + A KA+ Sbjct: 364 ADEFLAAFEKAV 375 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: 316 Number of extensions: 10 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: 382 Length adjustment: 32 Effective length of query: 427 Effective length of database: 350 Effective search space: 149450 Effective search space used: 149450 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