Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate CCNA_00196 CCNA_00196 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >FitnessBrowser__Caulo:CCNA_00196 Length = 479 Score = 202 bits (514), Expect = 2e-56 Identities = 148/447 (33%), Positives = 213/447 (47%), Gaps = 69/447 (15%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGAAEFQRVTRE 89 +DL + H+ T+P + F + + G R P+R + V DHN+P A V E Sbjct: 27 IDLHLIHEVTTP---QAFAGLRAAGRKVR--RPDRTLAVADHNIPTEG-QALGVDAVADE 80 Query: 90 FAREQGIVNIFQNAA--------------GICHQVLPERGFVRPGMVIVGADSHTCTYGA 135 AR Q + + +N A GI H V PE+G +PGM IV DSHT T+GA Sbjct: 81 EARLQ-LKTLARNVADNGIEFFPMGDIRNGIVHVVGPEQGRTQPGMTIVCGDSHTSTHGA 139 Query: 136 FGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGA 195 FGA A G+G +++ V AT + M + V G+ V KDV L +IGEIG G Sbjct: 140 FGALAHGIGTSEVEHVLATQTLRQKKAKNMLVRVDGQLPPGVTGKDVALAVIGEIGTAGG 199 Query: 196 TYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRARTG-------- 247 T +EF G+ I + + GRMT+CN+ +E GAK G++ P+ +T Y++ + Sbjct: 200 TGYVIEFAGEAIAGLSMEGRMTLCNLTIEGGAKAGLVAPDDKTFAYIQGKPAAPKGAAWD 259 Query: 248 ---REFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPV---------------- 288 ++ + +DED+ + D S L P V ++V PV Sbjct: 260 MALSHWKTFFTDEDAVFDRTVVIDGSALVPMVTWGTSPEDVIPVTGNVPDPESFATPDKR 319 Query: 289 ---HR------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIGD-----RRVHEDV 328 HR + ID F+GSCTN R ED++ AA V+ + R V V Sbjct: 320 AAAHRALDYMGLKAGQPISEARIDRVFIGSCTNSRIEDMRAAAAVVQEAFLHGRLVAPHV 379 Query: 329 RFIVSPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRN 388 + +V P S + +A E+G+ F AG PGC CL + LAP E +T+NRN Sbjct: 380 KAMVVPGSGLVKEQAEEEGLDAIFKAAGFDWREPGCSMCLAMNPDKLAPQERCASTSNRN 439 Query: 389 FRGRMGDPASSVYLANPAVVAESAIEG 415 F GR G A +L +PA+ A +AI G Sbjct: 440 FEGRQG-RAGRTHLVSPAMAAAAAIAG 465 Score = 24.3 bits (51), Expect = 0.009 Identities = 17/54 (31%), Positives = 26/54 (48%) Query: 371 HMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAPQQEA 424 +MG+ A +S A +R F G + A AVV E+ + G + AP +A Sbjct: 328 YMGLKAGQPISEARIDRVFIGSCTNSRIEDMRAAAAVVQEAFLHGRLVAPHVKA 381 Lambda K H 0.320 0.137 0.408 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: 577 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 428 Length of database: 479 Length adjustment: 33 Effective length of query: 395 Effective length of database: 446 Effective search space: 176170 Effective search space used: 176170 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 (21.8 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