Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF2189 PS417_11165 omega amino acid--pyruvate aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__WCS417:GFF2189 Length = 431 Score = 271 bits (694), Expect = 2e-77 Identities = 163/434 (37%), Positives = 244/434 (56%), Gaps = 18/434 (4%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 PFT + N + + +A G++ +EG +LDAMAGLWCVN G+G+ +V+A Sbjct: 8 PFTAMRPFNRQ-PMLFDRAAGMHYTTTEGRDVLDAMAGLWCVNAGHGQPRIVEAIREAAG 66 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143 L F + F + +HP + LA + AP ++ VFFT SGSEA DT L++ R Y +G Sbjct: 67 RLDFVSSF-KMSHPAALTLADQLVAKAPANLDKVFFTNSGSEAVDTALKIARAYHQARGD 125 Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDF-PIPG-IVHIAQPYWYGEGGDMSPD 201 ++ +IGR GYHG G+S+ G+ ++ DF P+ G + H+ PY G + Sbjct: 126 SRRTKLIGRAKGYHGMGFGGLSVSGIG--RQKRDFGPLLGDVAHLPLPYDAGSRFSLGQP 183 Query: 202 EFGVWAAEQLEKKILEVGEE-NVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFI 260 E G A+ L +LEV + VAA I EP+ G+GGV PP Y K+REI ++ +L I Sbjct: 184 EQGAHYADAL-LHLLEVHDPATVAAVIVEPVTGSGGVYAPPLGYLQKLREICDRHGLLLI 242 Query: 261 ADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG--- 317 DEVI GFGR G F ++ +G PDLM +AKGLT+G +PMGGV+V + E QG Sbjct: 243 FDEVITGFGRVGHGFAAEAFGVTPDLMTLAKGLTNGAVPMGGVLVSGAVYEAFMQGPEQA 302 Query: 318 -EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEAR 376 E HG+TYS HP+A A L + + E + V+ + AP Q L + LV + R Sbjct: 303 IELMHGYTYSAHPLACAAGLATLEVHEELGLNAHVR-QIAPLWQNTALALREQALVLDVR 361 Query: 377 GVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQI 436 +G++ A+EL K ++ GV + CF G+++RA G+ +++SPPL+I+ Q+ Sbjct: 362 AIGLLCAVEL-KPREGAPGARAAGVA----QRCFEAGVLVRASGENIVLSPPLIINQEQV 416 Query: 437 DELITLARKCLDQT 450 ++ + K L+ T Sbjct: 417 AQVFSTLGKALEAT 430 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: 563 Number of extensions: 35 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: 431 Length adjustment: 32 Effective length of query: 424 Effective length of database: 399 Effective search space: 169176 Effective search space used: 169176 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