Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000566685.1:WP_025763135.1 Length = 384 Score = 190 bits (483), Expect = 6e-53 Identities = 132/384 (34%), Positives = 204/384 (53%), Gaps = 31/384 (8%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 L D G E++D GG + +VGH +P V+ + QL+K +S + P + LA L Sbjct: 23 LWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSVQIPQQEELATKLGT 82 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKST 195 L+ F CNSG E+ E ALKLA + G+ +A + AFHG++ GA++AT + Sbjct: 83 LSGYPDYKLFLCNSGAEANENALKLASFHT---GRKKVVAFTKAFHGRTAGAVAATDNPS 139 Query: 196 FRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLT 255 P + +PF +IEA++ + E +VAAVI+E IQG GG+ + +L Sbjct: 140 IVAP-VNYNEHVSFLPFNDIEALQAGITE------EVAAVIVEGIQGVGGIQVCSDEFLQ 192 Query: 256 AVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIAT 315 A+RK CDE GA +ILD VQ G GRTGK F+ + + PD++ +AK +G G G IA Sbjct: 193 ALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHPDMMTMAKGMGNGFPIAGVLIAP 252 Query: 316 EEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAR 375 + F F L TTFGGN LACAA +A ++++ ++ L A + G L +L Sbjct: 253 Q--FKASFG---LLGTTFGGNHLACAAGIAVLDIMKDEQLLDNATKIGAYLFHEIEELG- 306 Query: 376 EYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVL----VAGTLNNAKTIRIEPPL 431 Y DL RG+G+++ IEF +F + R ++L + + A T+R+ P L Sbjct: 307 GYKDL----RGRGLMIGIEF-------DFPVKELRNKLLFEHHIFTGVAGAYTLRLLPSL 355 Query: 432 TLTIEQCELVIKAARKALAAMRVS 455 ++ ++ + ++A R L + S Sbjct: 356 AISQKEADQFLEAYRSCLKTFQQS 379 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: 15 Number of successful extensions: 6 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: 384 Length adjustment: 32 Effective length of query: 427 Effective length of database: 352 Effective search space: 150304 Effective search space used: 150304 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 24 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