Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PfGW456L13_1398 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1398 Length = 456 Score = 493 bits (1268), Expect = e-144 Identities = 230/449 (51%), Positives = 324/449 (72%), Gaps = 4/449 (0%) Query: 6 TNAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCV 65 T TR++QA HH+ F D K LN++G R++ + E +++WD++G + LD M+GLWC Sbjct: 3 TPRDTRDYQAADAAHHIHAFVDQKALNDEGPRVMVRGERLHLWDNDGRRYLDGMSGLWCT 62 Query: 66 NVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSE 125 N+GYGR++L AA+RQ+ +LP+YN+FF T HP V+EL++ + + P +H +T SGSE Sbjct: 63 NLGYGRKDLAAAASRQLEQLPYYNMFFHTTHPQVIELSELLFSLLPAHYSHAIYTNSGSE 122 Query: 126 ANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVH 185 AN+ ++R VR YW G+P+KK++IGRWNGYHGST+A +LGGMK +HE G IP I H Sbjct: 123 ANEVLIRTVRRYWQVLGKPEKKIMIGRWNGYHGSTLAATALGGMKFMHEMGGM-IPDIEH 181 Query: 186 IAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYW 245 I +PY++ G+++P EFG+ AA+QLE KILE+G + VA FIAEP QGAGG+I PP++YW Sbjct: 182 IDEPYFFAHEGNLTPAEFGLRAAQQLEAKILELGADKVAGFIAEPFQGAGGMIFPPESYW 241 Query: 246 PKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVV 305 P+I+ I KYD+L ADEVI GFGRTGEWF +Y+G PD + IAKGLTSGYIPMGG+++ Sbjct: 242 PEIQRICRKYDVLLCADEVIGGFGRTGEWFAHEYFGFEPDTLSIAKGLTSGYIPMGGLIL 301 Query: 306 RDEIVEVL-NQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQ 364 ++ VL QGG F HG TYSGHPVAAAVA+ N++ LR+E ++ +VK + PYLQ+ + Sbjct: 302 SKKMASVLVEQGGVFAHGLTYSGHPVAAAVAIANLKALRDEGVVTRVKDDIGPYLQQCLR 361 Query: 365 EL-ADHPLVGEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDT 422 E+ HPLVG+ +G GMVAAL+L ++K +R+RF ++ + CR F G+I+R+ Sbjct: 362 EVFGKHPLVGDIQGTGMVAALQLAEDKTSRKRFANENDIAWRCRTIGFEEGVIIRSTLGR 421 Query: 423 MIISPPLVIDPSQIDELITLARKCLDQTA 451 MI++P L+ +IDELI K +D+TA Sbjct: 422 MIMAPALIASREEIDELIAKTLKAVDRTA 450 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: 676 Number of extensions: 37 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: 456 Length adjustment: 33 Effective length of query: 423 Effective length of database: 423 Effective search space: 178929 Effective search space used: 178929 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