Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate RR42_RS27405 RR42_RS27405 aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Cup4G11:RR42_RS27405 Length = 448 Score = 352 bits (904), Expect = e-101 Identities = 189/426 (44%), Positives = 261/426 (61%), Gaps = 9/426 (2%) Query: 21 HLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATR 80 HL PFT+ G +ITK +G+Y+ D +G + L+ M+GLWC ++G+ +++A Sbjct: 15 HLHPFTNLAAHPGVGPLVITKGDGIYVEDDQGKRYLEGMSGLWCSSLGFSHARVIEAGVE 74 Query: 81 QMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWAT 140 MR LP+Y+ F ++P + LA+ + +AP M+ VFF SGSEANDT +++V +Y Sbjct: 75 AMRTLPYYHTFNHRSNPAAIMLAEKLVAMAPVPMSKVFFANSGSEANDTAVKLVWYYHNA 134 Query: 141 KGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP--YWYGEGGDM 198 G+P KK +I R N YHG TVA SL G++A H D PI I+ P Y YG G+ Sbjct: 135 IGKPDKKKIIARTNAYHGVTVAAASLSGLQANHRDFDLPIDRILRAGCPHHYRYGAPGE- 193 Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258 S F A++LE I G + + AFIAEP+ GAGGVIVPP TY+ +I+ +L ++DIL Sbjct: 194 SEAAFASRLAQELEALIQAQGPDTIGAFIAEPVMGAGGVIVPPATYFAEIQAVLRRHDIL 253 Query: 259 FIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVL--NQG 316 IADEVICGFGRTG FGS YG PD++ AK L+SGY+P+ V+V +++ + N G Sbjct: 254 LIADEVICGFGRTGAMFGSTTYGMRPDILTCAKALSSGYMPISAVMVSEKVHAAIAANSG 313 Query: 317 --GEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGE 374 G F HGFTYSGHPV AVALE +R+ +++I++ V A AP Q+ Q A LVGE Sbjct: 314 KIGTFGHGFTYSGHPVTTAVALETLRVYEDDRILDHVNA-IAPRFQQALQAYAGRALVGE 372 Query: 375 ARGVGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDP 433 RGVG++ A+EL R F G + GLI+RA+GDT+ PPL+I Sbjct: 373 VRGVGLLGAIELAAEPAARRAFDPALKAGPRLAQLAQEQGLIVRAMGDTIAFCPPLIITE 432 Query: 434 SQIDEL 439 +QI EL Sbjct: 433 AQIGEL 438 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: 548 Number of extensions: 24 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: 448 Length adjustment: 33 Effective length of query: 423 Effective length of database: 415 Effective search space: 175545 Effective search space used: 175545 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