Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BPHYT_RS23155 BPHYT_RS23155 aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__BFirm:BPHYT_RS23155 Length = 482 Score = 558 bits (1437), Expect = e-163 Identities = 259/445 (58%), Positives = 342/445 (76%), Gaps = 3/445 (0%) Query: 10 TREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGY 69 T E++AL HH+ PF+D LN G+R+I KA+GVY+WDSEGNK++D MAGLWCVNVGY Sbjct: 32 TAEYRALDAAHHIHPFSDMGSLNRSGSRVIVKAQGVYLWDSEGNKVIDGMAGLWCVNVGY 91 Query: 70 GREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDT 129 GR+EL AA +QM+ELP+YN FF+T HPPV+EL+ +A++APE NH F+ SGSE NDT Sbjct: 92 GRKELADAAYKQMQELPYYNTFFKTTHPPVIELSALLAELAPEAFNHFFYCNSGSEGNDT 151 Query: 130 VLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP 189 VLR+V YWAT+G+ KK VI R NGYHGST+AG +LGGM +HEQ + IVHI QP Sbjct: 152 VLRIVHQYWATQGKHSKKFVISRKNGYHGSTIAGGTLGGMGYMHEQMPSKVENIVHIDQP 211 Query: 190 YWYGEG-GDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKI 248 Y++GE G+++P+EF + A+QLE KILE+G +NVAAFI EP QGAGGVI P TYWP+I Sbjct: 212 YFFGEAQGNLTPEEFALARAQQLEAKILEIGADNVAAFIGEPFQGAGGVIFPASTYWPEI 271 Query: 249 REILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDE 308 + I KYDIL +ADEVI GFGRTGEWF Q++G PDL+ +AKGLTSGY+PMG V + D Sbjct: 272 QRICRKYDILLVADEVIGGFGRTGEWFAHQHFGFEPDLITLAKGLTSGYVPMGAVGLHDR 331 Query: 309 IVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQE-LA 367 + + + + G+F HG TYSGHPVAAAVA+ N+++LR+EKI+++VK +T PY QK+ +E A Sbjct: 332 VAKAIIENGDFNHGLTYSGHPVAAAVAVANLKLLRDEKIVDRVKNDTGPYFQKQLRETFA 391 Query: 368 DHPLVGEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDTMIIS 426 +HP++GE G G+VA L+L ++ K R+RF + G VG +CR+ CF LIMRA GD M++S Sbjct: 392 NHPIIGEISGTGLVAGLQLAQDPKARKRFANGGDVGTICRDFCFNGNLIMRATGDRMLLS 451 Query: 427 PPLVIDPSQIDELITLARKCLDQTA 451 PPLVI+ +IDE+++ A+K +D TA Sbjct: 452 PPLVINKLEIDEIVSKAKKAIDATA 476 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: 716 Number of extensions: 35 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: 482 Length adjustment: 33 Effective length of query: 423 Effective length of database: 449 Effective search space: 189927 Effective search space used: 189927 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