Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF3179 PGA1_c32300 aminotransferase class-III
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Phaeo:GFF3179 Length = 448 Score = 258 bits (659), Expect = 3e-73 Identities = 147/426 (34%), Positives = 230/426 (53%), Gaps = 6/426 (1%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 P T + + +IIT AEGV+I D +G++++D + GLW VN+GY + + A Q+ Sbjct: 18 PMTSPQDSVAQPPKIITGAEGVFITDIDGHRVIDGVGGLWNVNLGYSCQPVKDAMAAQLD 77 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADV-APEGMNHVFFTGSGSEANDTVLRMVRHYWATKG 142 +LP+Y+ F T++ +EL+ ++ P+G++ FFT GS++ +T LR+ R Y +G Sbjct: 78 KLPYYSTFRGTSNDAAIELSYELSRFFEPDGLSRAFFTSGGSDSVETALRLARQYHKLRG 137 Query: 143 QPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMS-PD 201 + + GYHG+ + G S+ G + +PG HI PY Y D S P+ Sbjct: 138 DSGRTKFLSLKKGYHGTHIGGASVNGNANFRTAYEPLLPGCFHIPAPYTYRNPFDESDPE 197 Query: 202 EFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIA 261 A LE +I G +AA I EPI GAGGVI P ++ P ++EI + IL I Sbjct: 198 RLAQLCAAALEDEIAFQGANTIAAMIMEPILGAGGVIPPHPSFAPMVQEICNRNGILLIT 257 Query: 262 DEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVL--NQGGEF 319 DEVI +GRTG W G++ +G PD+M AK +T+GY P G V++ ++EV N + Sbjct: 258 DEVITAYGRTGAWSGARLWGIQPDMMCTAKAITNGYFPFGAVMLGARMIEVFEDNPDAKI 317 Query: 320 YHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEAR-GV 378 HG+TYSGHPV AA AL + ++ + A A + ++G+ R G Sbjct: 318 GHGYTYSGHPVGAAAALTCLAEMQRLNVTATAAARGAQLYEGCLALKERFDVIGDVRGGY 377 Query: 379 GMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQIDE 438 G++ ALELV +++TR D + +E C+ G ++R G +I+SPPL++ + Sbjct: 378 GLMIALELVSDRQTRAPL-DGRRALALQEACYEAGALIRVSGPNVILSPPLIMSEADTRG 436 Query: 439 LITLAR 444 L+ R Sbjct: 437 LLDALR 442 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: 584 Number of extensions: 34 Number of successful extensions: 6 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