Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_013554936.1 NITSA_RS10120 succinyldiaminopimelate transaminase
Query= metacyc::MONOMER-6501 (397 letters) >NCBI__GCF_000186245.1:WP_013554936.1 Length = 379 Score = 243 bits (619), Expect = 9e-69 Identities = 143/384 (37%), Positives = 212/384 (55%), Gaps = 16/384 (4%) Query: 11 YPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLSVYPSTKGEPA 70 YPFEKL LL D P DL P++L+IGEP+ PA + Q + A L+ YP T GE Sbjct: 6 YPFEKLTQLLKDV-TPNPDLAPMSLTIGEPQFETPAFIRQELCDAAALLNKYPKTAGESY 64 Query: 71 LRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGALVVCPNPFYQIY 130 L++A+ +L +R+ + D +++P G+RE LF F Q + A + + PNPFYQIY Sbjct: 65 LKEAMRSYLKQRFGLEIAD--DQLIPTFGTRELLFNFPQFYLHDLADSTMAFPNPFYQIY 122 Query: 131 EGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAGNVMSLEEWRT 190 EGAA+ +GA +++ P F + +E LV + +P NP +VM E R Sbjct: 123 EGAAIASGARILHLDLTPENGF---QPPIDEEALSGCDLVILNTPNNPTASVMPFEAMRR 179 Query: 191 LFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVAFSSLSKRSNVP 250 L+ H F + ECY +++L P + L+A+ G + N+ +S+SKRS+ P Sbjct: 180 WVRLALEHDFFLLNDECYIDLWLKGPLPSM--LEASLAEGNSEFRNVAVVNSVSKRSSAP 237 Query: 251 GMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRKTAQYRAKFEAVL 310 G+RSGF+AGD +L +L YRTY G A + A+ AW+ + + +RAK+ Sbjct: 238 GLRSGFIAGDREVLREYLRYRTYVGCASPLPLQRAAARAWADQ---QHVEGFRAKYRRNF 294 Query: 311 PILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLLAREAHNANPGQGR 370 + + +L V AP+A+FY+W G + AF RELY R + VLPGS L R G+G Sbjct: 295 ELAEKILGVEAPEATFYIWMEV-GDELAFTRELYRRYNLKVLPGSFLGRN----GVGRGY 349 Query: 371 IRIALVAPLDQCVQAAERIAHFAR 394 +R+ALV + +A ER+A F R Sbjct: 350 VRLALVYEEEPMREALERVAAFIR 373 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: 429 Number of extensions: 28 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: 379 Length adjustment: 30 Effective length of query: 367 Effective length of database: 349 Effective search space: 128083 Effective search space used: 128083 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