Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate Pf6N2E2_1742 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1742 Length = 463 Score = 338 bits (867), Expect = 2e-97 Identities = 180/440 (40%), Positives = 263/440 (59%), Gaps = 8/440 (1%) Query: 21 HLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATR 80 HL T+ + + G +I + G+Y+ D G ++ M+GLWC +G+ LVQAA R Sbjct: 20 HLHSQTNLRAHQQHGPLVIERGSGIYVTDEHGRDYIEGMSGLWCAGLGFSNPRLVQAAQR 79 Query: 81 QMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWAT 140 QM LP+Y+ F V +LA+ IA + P VFF SGSEAND+++++ Y Sbjct: 80 QMAVLPYYHTFNHRVPNVVAQLAERIASLVPFEKPKVFFACSGSEANDSMVKLAWAYHRA 139 Query: 141 KGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPG-IVHIAQPYWYGEGGD-M 198 +G K+ +I G+HGSTV G SL G+ +H P+ ++H+ P++Y G + Sbjct: 140 RGNDGKRKIIAHQKGFHGSTVMGASLSGLPNMHAAFGLPLENSVLHVQCPHFYRHGIEGE 199 Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258 S +F LE++I G + +AAFI+EP+ GAGGVIVPP Y+ ++ +L K+DIL Sbjct: 200 SEAQFTERLLRDLEQRIEAEGADTIAAFISEPVMGAGGVIVPPPGYFVGVQALLKKHDIL 259 Query: 259 FIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVL----N 314 F+ADE+ICGFGRTG WFG Q G PD+M AK L+SGY P+ VVV + + +V+ Sbjct: 260 FLADEIICGFGRTGRWFGHQTLGFTPDMMACAKSLSSGYQPISCVVVAENVYQVIEEQSQ 319 Query: 315 QGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGE 374 Q G F HGFTYSGHPVAAAVALE + + +E + ++ + E L ++ + L HPL+GE Sbjct: 320 QLGGFGHGFTYSGHPVAAAVALETLTLYQEMHLPQRTE-ELGRLLHQQLEPLLAHPLIGE 378 Query: 375 ARGVGMVAALELVKNKKTRERF-TDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDP 433 RG+G+VA LELV +K TR F + +G+ GLI+R +GD++ ++PP +I Sbjct: 379 VRGIGLVAGLELVVDKHTRAPFPREIAIGVQVERAAREQGLIVRNMGDSIALAPPFIISA 438 Query: 434 SQIDELITLARKCLDQTAAA 453 +I EL+ + LD A A Sbjct: 439 EEIVELVARLTRALDAVALA 458 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: 602 Number of extensions: 26 Number of successful extensions: 5 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: 463 Length adjustment: 33 Effective length of query: 423 Effective length of database: 430 Effective search space: 181890 Effective search space used: 181890 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