Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate 3606628 Dshi_0060 aminotransferase class I and II (RefSeq)
Query= metacyc::MONOMER-6501 (397 letters) >FitnessBrowser__Dino:3606628 Length = 393 Score = 243 bits (619), Expect = 9e-69 Identities = 153/378 (40%), Positives = 199/378 (52%), Gaps = 12/378 (3%) Query: 4 RLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLSVYP 63 R AL Y F +LRALL D P + +SIGEP+H P A+A L + YP Sbjct: 6 RFSALPEYAFPRLRALL-DGHPPGGST--LAMSIGEPQHPFPQIATDALAEALPLFNKYP 62 Query: 64 STKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVI-DPSAGA--LV 120 G P L AI+ W+ RY + DP +VL + G+RE LFA + D AG LV Sbjct: 63 PNDGAPELCAAIADWVQGRYGVKL-DPARQVLALNGTREGLFAACLALCPDTKAGGQPLV 121 Query: 121 VCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAG 180 PNPFYQ+Y A AGA P +VNA F +P E R + +VCSP NP G Sbjct: 122 AMPNPFYQVYAVGAQAAGARPLFVNATAETGFLPNLTTLPPETLDRIAIAYVCSPSNPQG 181 Query: 181 NVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVAF 240 V WR L L+++H F + A ECY+EIY +TPP G+L+ A +G D +V F Sbjct: 182 AVADAGYWRALIGLAEKHDFYVFADECYAEIY--RETPPCGALEIATAMGADP-ERVVIF 238 Query: 241 SSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAW-SMRRMCRKT 299 SLSKRSN+PG+RSGF AG +A R Y G+ + + + A W + Sbjct: 239 HSLSKRSNLPGLRSGFAAGGPRAMAEMKKLRAYAGAPLPGPLHPVATAVWRDEAHVVENR 298 Query: 300 AQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLLAR 359 A Y AKF+ IL V +P A F+LW + A A +L+ TGV VLPG+ L+R Sbjct: 299 ALYAAKFDTADTILGAVPGYTSPAAGFFLWLPVEDGEAA-ALKLWTETGVRVLPGAYLSR 357 Query: 360 EAHNANPGQGRIRIALVA 377 + NPG G IR+ALVA Sbjct: 358 DTETGNPGAGFIRVALVA 375 Lambda K H 0.321 0.135 0.412 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: 532 Number of extensions: 24 Number of successful extensions: 8 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: 397 Length of database: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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