Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_043742980.1 AMB_RS00085 aspartate aminotransferase
Query= metacyc::MONOMER-6501 (397 letters) >NCBI__GCF_000009985.1:WP_043742980.1 Length = 399 Score = 251 bits (642), Expect = 2e-71 Identities = 158/398 (39%), Positives = 213/398 (53%), Gaps = 18/398 (4%) Query: 1 MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60 ++ RLD L YPF +L LL +P + +SIGEP+H PA V + +AAN + Sbjct: 7 LDARLDGLPDYPFARLAKLLGAPARPDSTV----MSIGEPQHRPPALVAEVLAANTSSWG 62 Query: 61 VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAG- 117 YP G LRQA++ W RRY +P DPE +LPV G+REAL+ AQTV G Sbjct: 63 KYPPANGPAELRQAVADWAGRRYDLPQGLIDPEKAILPVAGTREALYLIAQTVCGDREGQ 122 Query: 118 -ALVVCPNPFYQIYEGAALLAGATPYYVNA--DPARDFGLRTGRVPDEVWRRTQLVFVCS 174 LV+ PNPFYQ+Y GAA++AGA P +V PA T +P ++ RT L +VCS Sbjct: 123 RPLVLMPNPFYQVYAGAAVMAGAEPVFVPGANGPASQPDFST--LPADLLDRTALAYVCS 180 Query: 175 PGNPAGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRY 234 P NP G+V + HGFV+A ECYSEI+ + PP G L+ LG + Sbjct: 181 PANPQGSVADAALLERQVRTARDHGFVLAVDECYSEIW--DKVPPPGVLKTCAALG-EGL 237 Query: 235 TNLVAFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAW-SMR 293 N++ F+SLSKRS+VPG+RSG V GD ++ F R+Y G+A ++AA+ A W Sbjct: 238 ANVLMFNSLSKRSSVPGLRSGVVVGDERVIHAFARLRSYGGAATPLPIAAAAAALWRDEA 297 Query: 294 RMCRKTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLP 353 + YRAK + +L P F+LW G A A +L+ + VLP Sbjct: 298 HVTESNDLYRAKLDVAERVLGGRFGFYRPPGGFFLWLDV-GDGEAAAVKLWQEGNIRVLP 356 Query: 354 GSLLARE-AHNANPGQGRIRIALVAPLDQCVQAAERIA 390 G+ LA E + NPG IR+ALV L A R+A Sbjct: 357 GAYLAAEDSEEGNPGSRFIRVALVHDLAGTEAALTRLA 394 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: 551 Number of extensions: 34 Number of successful extensions: 9 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: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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