Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_013258997.1 DEBA_RS10935 aconitate hydratase
Query= SwissProt::Q9ZNE0 (418 letters) >NCBI__GCF_000143965.1:WP_013258997.1 Length = 639 Score = 200 bits (509), Expect = 9e-56 Identities = 142/420 (33%), Positives = 206/420 (49%), Gaps = 14/420 (3%) Query: 1 MGQTLAEKILS-HKVGRPVRAGELVVVEVDQVMVVDSIAGSFFKRLEYLEATPRYPERVS 59 M +TLA KI+ H V + GE + + +DQ + D+ E L R VS Sbjct: 1 MAKTLARKIIEEHLVEGRCQPGEEIGLRIDQTLTQDATGTLAALEFEAL-GLERVRTEVS 59 Query: 60 I-VIDHVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWVVVGS 118 + +DH ++ + + +R R+G+ G G+CHQ+ + +PG ++GS Sbjct: 60 VSYVDHNILQSDFKNPDDHRFLRSIAARYGLWFSPPGNGICHQLHMLN-FGRPGATLLGS 118 Query: 119 DSHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLPKGVTAKDAALEM 178 DSH+ G +G G G D+A A A +L P+ + V G+L V AKD LE+ Sbjct: 119 DSHTPHGGGLGMLAMGAGGLDVAAAMAGQPFFLTYPKVLGVRLSGKLSPWVGAKDVILEL 178 Query: 179 VRLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSGEILEMY--- 235 +R L+ +G VE H G L+ +R + N+ E GA + V PS E + + Sbjct: 179 LRRLSVKGGLGYVVEYHG-PGVTGLSVLQRAAITNMGAELGATSS-VFPSDEKTKAFLTA 236 Query: 236 --RVPDW--LYPDPDARYAKEVEIDLSALTPRVSVPFYVDNVHEVAQVKGKRVDQVFIGT 291 R W + D A Y K EIDL+AL P + P D V V ++ V+QV +G+ Sbjct: 237 QGRADAWREMSADDGAVYDKLEEIDLAALEPLAACPSSPDAVRPVRELAEVAVEQVIVGS 296 Query: 292 CTNGRIEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPG 351 C G EDL A L+G+ +AP + L V P S Q L + +G LL +LEAG + G Sbjct: 297 CGGGSYEDLMTIAMALKGKALAPGLNLSVNPGSRQALAQVTANGALLDMLEAGVRLHQAG 356 Query: 352 CGPCMGRHMGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPEEL 411 C C+G A G V T RNF GR G D +YL P VAAA+A+AG+L P ++ Sbjct: 357 CLGCIGMSQAP-ATGAASVRTFPRNFPGRSGTKDDRVYLTGPEVAAATALAGHLADPRQV 415 Lambda K H 0.318 0.135 0.393 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: 606 Number of extensions: 45 Number of successful extensions: 4 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: 418 Length of database: 639 Length adjustment: 35 Effective length of query: 383 Effective length of database: 604 Effective search space: 231332 Effective search space used: 231332 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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