Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate H281DRAFT_06342 H281DRAFT_06342 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Burk376:H281DRAFT_06342 Length = 473 Score = 335 bits (858), Expect = 2e-96 Identities = 185/443 (41%), Positives = 258/443 (58%), Gaps = 13/443 (2%) Query: 18 RDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQA 77 R H + P +Y+ +G ++ A G ++ D+ GN++LDA +GLWCVNVGYG++ +V+A Sbjct: 11 RQHLIHPVINYRAHEARGVTVLESASGAFLRDAAGNELLDAFSGLWCVNVGYGQQSIVEA 70 Query: 78 ATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHY 137 AT QM++LP+ +F P +ELA+ +A VAP + HV+FT GS+A D+ +R + HY Sbjct: 71 ATAQMKKLPYATSYFHFGSEPAIELAQKLASVAPASLQHVYFTLGGSDAVDSAIRFITHY 130 Query: 138 WATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGD 197 + G+P KK +I GYHGS+ G L + A H D P+P H+ PY Y Sbjct: 131 FNATGRPSKKHIIALQRGYHGSSSMGAGLTALPAFHRNFDLPLPNQHHLPSPYAYRSN-- 188 Query: 198 MSPDEFGVWAAE--QLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKY 255 D+ + AA LE K+ E+G +NVAAF EPIQG+GGVIVPP + +RE K Sbjct: 189 -FADDAALIAASVAALEAKVAELGADNVAAFFCEPIQGSGGVIVPPFGWLKAMRESCRKL 247 Query: 256 DILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQ 315 ILF+ADEVI GFGRTG F Q PDLM +AKGLT+GY PMG V++ DEI + + Sbjct: 248 GILFLADEVITGFGRTGPLFACQGESVEPDLMTVAKGLTAGYAPMGAVLMSDEIYQGIAD 307 Query: 316 GGE---FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLV 372 G HG TYS HPV+AA+ LE +R+ E ++ A AP + L +HPLV Sbjct: 308 GDAEAIVGHGHTYSAHPVSAAIGLEVLRLYHEGGLLAN-GAARAPRFARGLDALLEHPLV 366 Query: 373 GEARGVGMVAALELVKNKKTRERFTDKGVGMLCR--EHCFRNGLIMRAVGDTMI-ISPPL 429 G++R G++ ALELV NK ++ +F D + + R + N LI RA GD ++ +P L Sbjct: 367 GDSRHRGLLGALELVSNKDSKAQF-DPALKLSERIAAAAYENRLIFRAFGDNILGFAPAL 425 Query: 430 VIDPSQIDELITLARKCLDQTAA 452 S D + K LD A Sbjct: 426 SYTESDFDMMFERLEKTLDDVLA 448 Lambda K H 0.320 0.138 0.425 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: 518 Number of extensions: 18 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: 456 Length of database: 473 Length adjustment: 33 Effective length of query: 423 Effective length of database: 440 Effective search space: 186120 Effective search space used: 186120 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