Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate RR42_RS01530 RR42_RS01530 isopropylmalate isomerase
Query= SwissProt::Q9ZNE0 (418 letters) >FitnessBrowser__Cup4G11:RR42_RS01530 Length = 472 Score = 224 bits (572), Expect = 3e-63 Identities = 151/416 (36%), Positives = 213/416 (51%), Gaps = 60/416 (14%) Query: 55 PERVSIVIDHVAPAANLEVAKAQ--------KEIREWGKRHGIRVFDVG---RGVCHQVL 103 P + V+DH+ P + Q + ++ +HGI +FD +G+ H + Sbjct: 55 PGQQVAVVDHIIPTHAESPRRIQDPASALQARNLKRNCDQHGIPLFDTDDALQGIEHVIA 114 Query: 104 IEEGLAQPGWVVVGSDSHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRG 163 E G+ +PG VV+ DSH+TTYGA+GA G G+G +++ A+ RV +++ G Sbjct: 115 PEHGMIRPGMVVLCGDSHTTTYGALGALGFGIGTSEVEHVLATQTLVYRVAMDMRIRVDG 174 Query: 164 RLPKGVTAKDAALEMVRLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAG 223 LP G TAKD L ++ ++A+GA VE AL+ RMTL N+TVEAGA+ Sbjct: 175 VLPCGATAKDMILHIISRISAQGARGYVVEF-TGSAIAALSIEARMTLCNMTVEAGARGA 233 Query: 224 LVVPSGEILE--MYRVPD------------W--LYPDPDARYAKEVEIDLSALTPRVS-- 265 L+ P +E + R D W L+ D DAR+ E+ D S + P VS Sbjct: 234 LIAPDAAAIEYVLARAADIDATLRERALACWRALHSDADARFDSELVFDASNVAPYVSWG 293 Query: 266 ------------VPFYVDNVHEVAQ-----------------VKGKRVDQVFIGTCTNGR 296 VP D + + A+ ++G V +VFIG+CTNGR Sbjct: 294 TSPDQAIPIDACVPPVEDAIDDTARSAAAKALDYIGLQAGATLEGLPVQRVFIGSCTNGR 353 Query: 297 IEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGCGPCM 356 IEDLRA A ++RGRKVA VR +VVP S V ++A +G LL+AG PGC C+ Sbjct: 354 IEDLRAVAAIVRGRKVAAGVRAMVVPGSGAVRQQAEDEGIAQVLLDAGFEWRKPGCSMCL 413 Query: 357 GRHMGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPEELE 412 + VLAPGE C ST+NRNF GR G +L SP +AAA+A+ G +T LE Sbjct: 414 AMNDDVLAPGERCASTTNRNFEGRQGRA-GRTHLMSPAMAAAAALTGCITDVRRLE 468 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: 463 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 418 Length of database: 472 Length adjustment: 32 Effective length of query: 386 Effective length of database: 440 Effective search space: 169840 Effective search space used: 169840 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