Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_007472961.1 CMTB2_RS00510 hypothetical protein
Query= metacyc::MONOMER-6501 (397 letters) >NCBI__GCF_000170735.1:WP_007472961.1 Length = 363 Score = 213 bits (542), Expect = 7e-60 Identities = 139/379 (36%), Positives = 204/379 (53%), Gaps = 24/379 (6%) Query: 11 YPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLSVYPSTKGEPA 70 YPFEKL LL D P I+L+IGEP+ P + + N+ L+ YP T GE Sbjct: 5 YPFEKLNELLKDIPHPDE---VISLTIGEPQFETPKFIQDELCKNVKYLNKYPKTAGEEV 61 Query: 71 LRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGALVVCPNPFYQIY 130 L++A ++ RRY+I + E+LP G+RE LF F + P A PNPFYQIY Sbjct: 62 LKKAQRDFVKRRYNIELE--KDELLPSFGTRELLFNFP-LFLKPKKTAF---PNPFYQIY 115 Query: 131 EGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAGNVMSLEEWRT 190 EGAA+ A + Y+ +F +P ++ V + SP NP +VM ++ Sbjct: 116 EGAAIAANSKINYMPLKKENNFL----SIPSQLDGDEDFVILNSPNNPTASVMDIDLLCE 171 Query: 191 LFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVAFSSLSKRSNVP 250 E + + FVI + ECYSEIY D+ P + L+A+ R+G + N++A +S+SKRS+ P Sbjct: 172 WVEEALKKDFVILSDECYSEIYFDKKPPSI--LEASIRVGNKNFKNVLAINSISKRSSAP 229 Query: 251 GMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRKTAQYRAKFEAVL 310 G+RSGF+AGD+ +L ++L +RTY G A + A+ AW +R K++ Sbjct: 230 GLRSGFIAGDSKILKKYLNFRTYVGCASPLPLQYAAAKAWMDD---EHVETFREKYKRNF 286 Query: 311 PILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLLAREAHNANPGQGR 370 I + +L + P+A+FY+W D F +E Y R GV V+PG + RE G G Sbjct: 287 EIAKEILGIEVPKATFYIWLEV-DDDIEFTKEAYKR-GVKVMPGRFMGREGE----GVGY 340 Query: 371 IRIALVAPLDQCVQAAERI 389 IRIALV ++ QA + I Sbjct: 341 IRIALVYNEEKTKQALKII 359 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: 347 Number of extensions: 18 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: 363 Length adjustment: 30 Effective length of query: 367 Effective length of database: 333 Effective search space: 122211 Effective search space used: 122211 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