Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_086509870.1 BZY95_RS10460 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_002151265.1:WP_086509870.1 Length = 485 Score = 591 bits (1523), Expect = e-173 Identities = 289/465 (62%), Positives = 357/465 (76%), Gaps = 20/465 (4%) Query: 10 TREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGY 69 T ++ L RDHHL PFTD+K L E+G+RI+T AEG+YI DSEGN+ILDAMAGLWCVN+GY Sbjct: 3 TETYRQLDRDHHLHPFTDFKALGEEGSRIVTHAEGIYIHDSEGNRILDAMAGLWCVNLGY 62 Query: 70 GREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDT 129 GREELV AAT Q+RELP+YN FF++ HPP V+LA+ + +AP MN VFFTGSGSEANDT Sbjct: 63 GREELVAAATAQLRELPYYNNFFKSTHPPAVKLAEMLCRLAPAHMNRVFFTGSGSEANDT 122 Query: 130 VLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP 189 VLRMVR YWA +G+P K+ VI R N YHGSTVAG+SLGGM +H QG +P I H+ QP Sbjct: 123 VLRMVRRYWALEGKPDKQWVIARENAYHGSTVAGLSLGGMAPMHAQGGPLVPKIAHVRQP 182 Query: 190 YWY----------GEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIV 239 YW+ GEG D SP+ FG A LE KIL +GEENVAAFIAEP+QGAGG I+ Sbjct: 183 YWFGEGKVAQGRVGEGRDTSPEAFGRECAAALEAKILALGEENVAAFIAEPVQGAGGAII 242 Query: 240 PPDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIP 299 PP +YWP ++E+LA+YDIL + DEVICGFGR GEWFGS +Y PDLMPIAKGL+SGY+P Sbjct: 243 PPQSYWPAVKEVLARYDILLVVDEVICGFGRLGEWFGSIHYDLKPDLMPIAKGLSSGYLP 302 Query: 300 MGGVVVRDEIVEVL-NQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPY 358 +GGV+V D + E L +GGEF+HGFTYSGHPV AAVAL+N+ +++ E I+E+V+ + PY Sbjct: 303 IGGVLVGDRVAETLIERGGEFFHGFTYSGHPVCAAVALKNLELMQAEGIVERVRDDVGPY 362 Query: 359 LQKRWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDK-------GVGMLCREHCFR 411 L +RW LADHPLVGE R +G++ ALEL+ + T ERF DK GVG LCR+ CF Sbjct: 363 LAERWATLADHPLVGEVRSLGLIGALELI-DPDTGERF-DKARFPKGFGVGTLCRDICFD 420 Query: 412 NGLIMRAVGDTMIISPPLVIDPSQIDELITLARKCLDQTAAAVLA 456 +GL+MR+VGDTMIISPPLVI ++IDEL+ LA + LD+TA + A Sbjct: 421 HGLVMRSVGDTMIISPPLVITRAEIDELVRLAWEALDETARRLAA 465 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: 804 Number of extensions: 38 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: 485 Length adjustment: 33 Effective length of query: 423 Effective length of database: 452 Effective search space: 191196 Effective search space used: 191196 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 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