Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PfGW456L13_3 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3 Length = 449 Score = 272 bits (696), Expect = 1e-77 Identities = 166/458 (36%), Positives = 249/458 (54%), Gaps = 23/458 (5%) Query: 3 SQITNAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGL 62 +Q NA T L D H P+T + ++ R+I AEG ++ D +G K+ D+++GL Sbjct: 2 NQPENAPTSLASQLKLDAHWMPYTANRNF-QRDPRLIVGAEGSWLIDDKGRKVYDSLSGL 60 Query: 63 WCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGS 122 W G+ R+E+ +A +Q+ L Y+ FQ HP +LA+ I D+ P +NHVFFT S Sbjct: 61 WTCGAGHTRKEIQEAVAKQLGTLD-YSPGFQYGHPLSFQLAEKITDLTPGNLNHVFFTDS 119 Query: 123 GSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGM---KALHEQGDFP 179 GSE DT ++MVR YW KGQ K +IGR GYHG +AG SLGG+ + L Q Sbjct: 120 GSECADTAVKMVRAYWRLKGQSTKTKMIGRARGYHGVNIAGTSLGGVNGNRKLFGQAMMD 179 Query: 180 IPGIVH-IAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVI 238 + + H + Y G P++ G+ A++L K I N+AA EP+ G+ GV+ Sbjct: 180 VDHLPHTLLASNAYSRG---MPEQGGIALADELLKLIELHDASNIAAVFVEPLAGSAGVL 236 Query: 239 VPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYI 298 VPP Y ++REI +++IL + DEVI GFGRTG FG+ +G PDLM IAK +T+G I Sbjct: 237 VPPQGYLKRLREICDQHNILLVFDEVITGFGRTGTMFGATTFGVTPDLMCIAKQVTNGAI 296 Query: 299 PMGGVVVRDEIVEV-LNQ-----GGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVK 352 PMG V+ EI + +NQ EF HG+TYS HPVA A L + +L++E +++ V Sbjct: 297 PMGAVIASSEIYQTFMNQPTPEYAVEFPHGYTYSAHPVACAAGLAALDLLQKENLVQSV- 355 Query: 353 AETAPYLQKRWQELADHPLVGEARGVGMVAALELV-KNKKTRERFTDKGVGMLCREHCFR 411 AE AP+ + L + + R G+ A+++ ++ R + G+ + ++ Sbjct: 356 AEVAPHFENALHGLKGTKNIIDIRNYGLAGAIQIAPRDGDAIVRPFEAGMAL------WK 409 Query: 412 NGLIMRAVGDTMIISPPLVIDPSQIDELITLARKCLDQ 449 G +R GDT+ P P +D L + L + Sbjct: 410 AGFYVRFGGDTLQFGPTFNSKPQDLDRLFDAVGEVLSK 447 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: 534 Number of extensions: 30 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: 449 Length adjustment: 33 Effective length of query: 423 Effective length of database: 416 Effective search space: 175968 Effective search space used: 175968 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