Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate AO356_27230 AO356_27230 hypothetical protein
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27230 Length = 871 Score = 264 bits (675), Expect = 8e-75 Identities = 173/433 (39%), Positives = 239/433 (55%), Gaps = 37/433 (8%) Query: 39 IEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGH 98 I F++HVNP E + V G D V G L D QG+ ++D LG +G GH Sbjct: 7 ISPFEQHVNPAVGELIRRV--GLDKTFVR---GEGCYLYDAQGRAYLDFLGAYGALPFGH 61 Query: 99 RNPVVVSAVQN-QLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAA 157 +++ + + QL+++P+ Q +LA+ L A+ PG + F NSG E+VEAA Sbjct: 62 SPDALLAELASFQLSREPIFVQPSSLAASGLLAQRLLAIAPGDYRSVTFQNSGAETVEAA 121 Query: 158 LKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEA 217 LK A G+ ++T +FHGK+LGALSAT +++ F LPGF V +G+I+A Sbjct: 122 LK---ACLIKTGRKRILSTHQSFHGKTLGALSATGSDKYQEGFQAPLPGFDFVDYGDIQA 178 Query: 218 MRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGM 277 + L ++ D AAVI+EP+QGEGG+ LPPP YL +R CD G L+I+DEVQTG+ Sbjct: 179 LEDQL---QRHPDAYAAVIIEPVQGEGGINLPPPEYLQQIRAACDRSGTLLIIDEVQTGL 235 Query: 278 GRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNP 337 GRTG+MFA VQ D L LAKALGGGVMPIGA + ++ +S F N H++TFGGN Sbjct: 236 GRTGQMFA--SAGVQADCLLLAKALGGGVMPIGACLISKNAYSEDFQNK--HSSTFGGNT 291 Query: 338 LACAAALATINVLLE-QNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFV 396 LAC L +++L E Q+L G LL+ +LA + ++E RG G L+ IEF Sbjct: 292 LACRIGLKVLDLLDERQDLLDSVRDNGRYLLEQLNELAARHASFIKEVRGAGYLIGIEFD 351 Query: 397 DNEIGY-----NFASEMFRQR---------------VLVAGTLNNAKTIRIEPPLTLTIE 436 + Y F M Q V VA TLN A +R+EPPL Sbjct: 352 LDRSHYPQFYGGFTGIMGEQESLVPILASYLLNVEGVRVAPTLNGANVMRVEPPLIAGRA 411 Query: 437 QCELVIKAARKAL 449 +CE+ I+A + L Sbjct: 412 ECEVFIQALARTL 424 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: 868 Number of extensions: 41 Number of successful extensions: 8 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: 871 Length adjustment: 38 Effective length of query: 421 Effective length of database: 833 Effective search space: 350693 Effective search space used: 350693 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: 54 (25.4 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