Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate 351388 BT1860 3-isopropylmalate dehydratase large subunit (NCBI ptt file)
Query= SwissProt::Q9ZNE0 (418 letters) >FitnessBrowser__Btheta:351388 Length = 464 Score = 200 bits (509), Expect = 7e-56 Identities = 142/415 (34%), Positives = 204/415 (49%), Gaps = 62/415 (14%) Query: 55 PERVSIVIDHVAPAANLE------VAKAQ-----KEIREWGKRHGIRVFDVGRGVCHQVL 103 PE+V + DH P + + ++K Q K +++G H + G+ H V Sbjct: 53 PEKVFCMPDHNTPTHDQDKPIEDPISKTQVDTLTKNAKDFGLTH-FGMMHPKNGIIHVVG 111 Query: 104 IEEGLAQPGWVVVGSDSHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRG 163 E L PG +V DSH++T+GA+GA G+G +++ + AS P+++++ G Sbjct: 112 PERALTLPGMTIVCGDSHTSTHGAMGAIAFGIGTSEVEMVLASQCILQSRPKTMRITVDG 171 Query: 164 RLPKGVTAKDAALEMVRLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAG 223 L KGVTAKD AL M+ +T GAT VE + LT R+TL NL++E GA+ G Sbjct: 172 ELGKGVTAKDVALYMMSKMTTSGATGYFVE-YAGSAIRNLTMEGRLTLCNLSIEMGARGG 230 Query: 224 LVVPSGEILEMYRVPD--------------W--LYPDPDARYAKEVEIDLSALTPRVS-- 265 +V P E + + W L D DA + +EV D + + P ++ Sbjct: 231 MVAPDEVTFEYIKGRENAPQGEAWDQAMEYWKTLKSDDDAVFDQEVRFDAADIEPMITYG 290 Query: 266 ------------VPFYVDNVHEVAQVK-----------------GKRVDQVFIGTCTNGR 296 +P + + E AQV GK++D VF+G CTNGR Sbjct: 291 TNPGMGMGITQNIPT-TEGMGEAAQVSFKKSMEYMGFQPGESLLGKKIDYVFLGACTNGR 349 Query: 297 IEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGCGPCM 356 IED RA A +++GR+ A V +VP S V + ++G L EAG I PGC C+ Sbjct: 350 IEDFRAFASLVKGRRKADNVIAWLVPGSWMVDAQIRKEGIDKILTEAGFAIRQPGCSACL 409 Query: 357 GRHMGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPEEL 411 + + G+ VSTSNRNF GR G P A LASP VAAA+AV G +T P EL Sbjct: 410 AMNDDKIPAGKYSVSTSNRNFEGRQG-PGARTLLASPLVAAAAAVTGVITDPREL 463 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: 459 Number of extensions: 27 Number of successful extensions: 3 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: 464 Length adjustment: 32 Effective length of query: 386 Effective length of database: 432 Effective search space: 166752 Effective search space used: 166752 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: 51 (24.3 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