Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_084276337.1 B8779_RS08925 hypothetical protein
Query= metacyc::MONOMER-6501 (397 letters) >NCBI__GCF_900176045.1:WP_084276337.1 Length = 373 Score = 233 bits (593), Expect = 9e-66 Identities = 141/385 (36%), Positives = 213/385 (55%), Gaps = 19/385 (4%) Query: 11 YPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLSVYPSTKGEPA 70 YPFEKL LL +P ++ P+ L+IGEP+ AAP + + + L+ YP T GE Sbjct: 6 YPFEKLTELLEKV-EPNNEYAPLTLTIGEPQFAAPKFIQDKLCQSSHLLNKYPKTAGEEE 64 Query: 71 LRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGALVVCPNPFYQIY 130 L++A+ ++ RR++I + E++ G+RE LF F Q + ++ NPFYQIY Sbjct: 65 LKKAVKDFVKRRFAIELTN--EELVLTFGTREVLFNFPQYFLFDKESPVMAFTNPFYQIY 122 Query: 131 EGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAGNVMSLEEWRT 190 EGAA+ + A Y++ DF + D+ + LV + SP NP +VM L+E + Sbjct: 123 EGAAIASRAKIKYLHLTKENDFKPQI----DDSLKEADLVIINSPNNPTASVMRLDELKE 178 Query: 191 LFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVAFSSLSKRSNVP 250 E + + FV+ ECYSEIY D PP L+A++ +G ++ N++ +S+SKRS+ P Sbjct: 179 WVEAALEYDFVLLNDECYSEIY--RDVPPASLLEASKAVGNTQFKNILVVNSISKRSSAP 236 Query: 251 GMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMR-RMCRKTAQYRAKFEAV 309 G+RSGF+AGD+ +L + YRTY G A + A+ AWS + +YR F+ Sbjct: 237 GLRSGFIAGDSKILDGYRRYRTYVGCASPLPLQRAAANAWSDELHVVENRDRYRKNFK-- 294 Query: 310 LPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLLAREAHNANPGQG 369 + +L+V P+A+FYLW D F +ELY + V VLPGS L RE G+G Sbjct: 295 --LAHEILNVAIPEATFYLWLEV-RDDLGFTKELYEKYNVKVLPGSFLGRE----GAGKG 347 Query: 370 RIRIALVAPLDQCVQAAERIAHFAR 394 +R+ALV + +A +RIA R Sbjct: 348 FVRVALVYDECKTEEALQRIAKLWR 372 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: 359 Number of extensions: 26 Number of successful extensions: 7 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: 373 Length adjustment: 30 Effective length of query: 367 Effective length of database: 343 Effective search space: 125881 Effective search space used: 125881 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 10 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