Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate PP_3721 PP_3721 Arginine--pyruvate transaminase AruH
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Putida:PP_3721 Length = 396 Score = 194 bits (493), Expect = 4e-54 Identities = 112/357 (31%), Positives = 194/357 (54%), Gaps = 5/357 (1%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L A+ +D++ L++G PDF TP + AA ++ T Y G L LRQA+ ++++ Sbjct: 27 LQAEDKDILLLSVGDPDFDTPAPIVEAAIDSLRAGHTHYADVRGKLALRQAIANRHRQRS 86 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 A+ ++ + GA A+ + IL PGDEVI+ P+Y YE + CGAK V V Sbjct: 87 GQAVSAD-QVTVLAGAQCALYCVAQCILDPGDEVIVAEPMYVTYEAVFGACGAKVVPVPV 145 Query: 143 T-SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDE 201 +GF++ R + + +TP T+ + L P NP+G +L +++A L +++++SDE Sbjct: 146 KPENGFRVCPRDVAERITPRTRALALNSPHNPSGASLPRATWEALAELCVAHDLWLISDE 205 Query: 202 IYSELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQY 259 +YSEL Y+ H S + + ++T +N LSKSH+MTGWR+G++ +A H+ + Sbjct: 206 VYSELLYEGEHVSPGSLPGMAERTATLNSLSKSHAMTGWRMGWVVGSTALATHLENLALC 265 Query: 260 NVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIF 318 + Q AA+ A+ + + MRE Y++R D V ++L GL +KP G ++ Sbjct: 266 MLYGLPDFVQDAAVVALEHPLPELDAMREAYRQRRDLVCEQLAGCPGLKALKPDGGMFVM 325 Query: 319 PSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRL 375 I+ G+++ F+ LL+ GV+++ G +F G++RL + L + R+ Sbjct: 326 LDIRETGVSAQAFADYLLDSQGVSVLAGEAFGPSAAGHIRLGLVLGNEALVDACQRI 382 Lambda K H 0.319 0.135 0.388 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: 296 Number of extensions: 12 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: 393 Length of database: 396 Length adjustment: 31 Effective length of query: 362 Effective length of database: 365 Effective search space: 132130 Effective search space used: 132130 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: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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