Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_011840202.1 RSPH17029_RS00745 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= metacyc::MONOMER-6501 (397 letters) >NCBI__GCF_000015985.1:WP_011840202.1 Length = 392 Score = 252 bits (643), Expect = 1e-71 Identities = 158/391 (40%), Positives = 213/391 (54%), Gaps = 15/391 (3%) Query: 4 RLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLSVYP 63 R L Y F +LR LL D P + P+ ++IGEPKH P VG +A +LAG +YP Sbjct: 6 RFSNLPDYAFPRLRKLL-DPHAPGGE--PVAMTIGEPKHPMPEFVGPVLAESLAGFGLYP 62 Query: 64 STKGEPALRQAISQWLSRRYSIPAPDPESEVLPVL-GSREALFAFAQTVIDPS---AGAL 119 G P L AI WL RRY + D E L VL G+RE LF A ++ + A + Sbjct: 63 PNDGTPELLSAIGGWLKRRYRV---DLGPERLMVLNGTREGLFNAALALVPETKRGARPV 119 Query: 120 VVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPA 179 V+ PNPFYQ+Y AAL GA P YV A + F +P E+ RT L ++CSP NP Sbjct: 120 VLMPNPFYQVYAMAALALGAEPVYVPALASNGFLPDYASLPAEILERTALAYLCSPANPQ 179 Query: 180 GNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVA 239 G+V S + W L +L++ H F + A ECY+EI+ PP G+L+ A G D + A Sbjct: 180 GSVASRDYWAGLMDLAETHDFRLFADECYAEIW--RTAPPAGALEVADATGADP-ERIFA 236 Query: 240 FSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWS-MRRMCRK 298 F SLSKRSN+PG+RSGFVAG +AR R + G+ + V S AW+ + Sbjct: 237 FHSLSKRSNLPGLRSGFVAGGPEGIARIRQLRAFAGAPLPLPVQRVSERAWADETHVEAN 296 Query: 299 TAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLLA 358 A Y+ KF + + P+ F+LW P + A A +L+ TGV VLPG+ LA Sbjct: 297 RALYQEKFRIADEVFSGLQGYMGPEGGFFLWLPVPDGEEA-ALKLWTETGVRVLPGAYLA 355 Query: 359 REAHNANPGQGRIRIALVAPLDQCVQAAERI 389 RE NPG+G IR+A+VAP D+ + R+ Sbjct: 356 REVGGENPGKGYIRVAMVAPKDEMQRGLVRL 386 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: 492 Number of extensions: 27 Number of successful extensions: 5 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 16 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