Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate H281DRAFT_01082 H281DRAFT_01082 putrescine aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Burk376:H281DRAFT_01082 Length = 478 Score = 547 bits (1409), Expect = e-160 Identities = 259/445 (58%), Positives = 332/445 (74%), Gaps = 3/445 (0%) Query: 10 TREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGY 69 T E++AL HH+ PF+D +LN G+R+I +A GVY+WDSEGNKI+D MAGLWCVNVGY Sbjct: 28 TAEYRALDAAHHIHPFSDMGELNRSGSRVIVRAHGVYLWDSEGNKIIDGMAGLWCVNVGY 87 Query: 70 GREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDT 129 GR+EL AA RQM ELP+YN FF+T HPPV+EL+ +A++APE NH F+ SGSEANDT Sbjct: 88 GRKELANAAYRQMEELPYYNTFFKTTHPPVIELSALLAELAPEPFNHFFYCNSGSEANDT 147 Query: 130 VLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP 189 VLR+V YW T+G+ KKVVI R NGYHGST+AG +LGGM +HEQ + IVHI QP Sbjct: 148 VLRIVHRYWTTQGKHSKKVVISRRNGYHGSTIAGGTLGGMGYMHEQMPSKVENIVHIDQP 207 Query: 190 YWYGE-GGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKI 248 Y++ E +P+EF + A+QLE KILE+G NVAAFI EP QGAGGVI P TYWP+I Sbjct: 208 YFFAEANSSQTPEEFALARAQQLEMKILEIGAHNVAAFIGEPFQGAGGVIFPASTYWPEI 267 Query: 249 REILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDE 308 I KYD+L +ADEVI GFGRTGEWF Q++G PDL+ +AKGLTSGY+PMG V + D Sbjct: 268 ERICRKYDVLLVADEVIGGFGRTGEWFAHQHFGFQPDLITMAKGLTSGYVPMGAVGLNDR 327 Query: 309 IVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQE-LA 367 I + + + GEF HG TYSGHPVAAAVA+ N+++LR+EKI+E+VK +T PY QK+ ++ A Sbjct: 328 IAKAIIENGEFNHGLTYSGHPVAAAVAVANLKLLRDEKIVERVKTDTGPYFQKKLRDTFA 387 Query: 368 DHPLVGEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDTMIIS 426 HP+VGE G G+VA L+L + +R+RF + G VG +CR+ CF LIMRA GD M++S Sbjct: 388 RHPIVGEIAGAGLVAGLQLAEEPASRKRFANGGDVGGVCRDFCFNGNLIMRASGDRMLLS 447 Query: 427 PPLVIDPSQIDELITLARKCLDQTA 451 PPLVI +ID+L++ A+ +D TA Sbjct: 448 PPLVISKQEIDDLVSKAKNAIDATA 472 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: 706 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: 478 Length adjustment: 33 Effective length of query: 423 Effective length of database: 445 Effective search space: 188235 Effective search space used: 188235 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