Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate GFF3277 PGA1_c33280 putative LL-diaminopimelate aminotransferase
Query= metacyc::MONOMER-6501 (397 letters) >FitnessBrowser__Phaeo:GFF3277 Length = 392 Score = 244 bits (624), Expect = 2e-69 Identities = 150/382 (39%), Positives = 211/382 (55%), Gaps = 12/382 (3%) Query: 4 RLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLSVYP 63 R L PY F +LRALL D P D+ ++++IGEPKH PA V I N AG YP Sbjct: 6 RFSNLPPYAFPRLRALL-DHHTPGGDV--VHMTIGEPKHDFPAWVTDVIVDNAAGFQSYP 62 Query: 64 STKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPS---AGALV 120 +G LR AIS W+ RRY + DP ++V+ + G+RE L+ A + A +V Sbjct: 63 PNEGSAELRGAISDWIKRRYDVSV-DPMTQVMALNGTREGLYNAAMALCPEQKNGAKPVV 121 Query: 121 VCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAG 180 + PNPFYQ+Y A++ A P +V A D +P EV RT + ++CSP NP G Sbjct: 122 LIPNPFYQVYMVASISVAAEPVFVPATADTDHLPDYVGLPPEVLNRTAVAYICSPANPQG 181 Query: 181 NVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVAF 240 V S W L +L++++ F I A ECYSEIY + P+G+L A+ LG D +V F Sbjct: 182 AVASRAYWTQLIQLAEQYDFRIFADECYSEIY--RASAPVGALSVAQELGADP-ERVVLF 238 Query: 241 SSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWS-MRRMCRKT 299 +SLSKRSN+ G+RSG +AG + R R Y G+ + + AA+ W+ + Sbjct: 239 NSLSKRSNLAGLRSGLIAGGPDTMKRVHQLRAYSGAPLPAPLQAAAARVWADEAHVTENR 298 Query: 300 AQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLLAR 359 A Y+ K+ + + AP+A F+LW + A A +L+ TGV VLPG+ LA+ Sbjct: 299 ALYQEKYRIADQVFDGLDGYMAPEAGFFLWLPVEDGEAA-ALKLWQDTGVRVLPGAYLAQ 357 Query: 360 EAHNANPGQGRIRIALVAPLDQ 381 ANPG+G IR+ALVAP +Q Sbjct: 358 GDGTANPGKGYIRVALVAPAEQ 379 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: 471 Number of extensions: 23 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: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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