Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate N515DRAFT_0572 N515DRAFT_0572 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >FitnessBrowser__Dyella79:N515DRAFT_0572 Length = 471 Score = 236 bits (601), Expect = 1e-66 Identities = 151/443 (34%), Positives = 226/443 (51%), Gaps = 58/443 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHN---VPANTIG------- 79 +DL + H+ TSP + F ++ RG R P+R + DH+ +PAN G Sbjct: 29 IDLHLVHEVTSP---QAFSELRERGLKLR--RPDRALATLDHSTPTLPANDKGERPYANE 83 Query: 80 -----AAEFQRVTREFAREQGIVNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYG 134 A+ + REF E + + GI H + PE G +PGM IV DSHT T+G Sbjct: 84 EAKAQVAQLEANCREFGVE--LHGWDSSERGIVHVIGPELGATQPGMTIVCGDSHTSTHG 141 Query: 135 AFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDG 194 AFGA A G+G T++ V AT P+ + I V G+ + AKD+ILHIIGEIGVDG Sbjct: 142 AFGALAFGIGTTEVGHVMATQCLLQRKPKTLAIHVDGQLPKGIGAKDLILHIIGEIGVDG 201 Query: 195 ATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRAR--------- 245 T +E+ G+ IE++ + RMT+CNM++E GA+ G++ P+ T +++ R Sbjct: 202 GTGHVIEYRGEAIEALSMDERMTVCNMSIEAGARAGLIAPDDTTFAWLKGRPRVPQGAAW 261 Query: 246 --TGREFRVYSSDEDSQYLEDHHFDVSDLEPQVACPD----------------------- 280 ++R +D + Y + D S ++P V Sbjct: 262 DAAVAKWRALRTDAGASYDREVRIDASKVKPTVTYGTHPGMAIAMDAPVPAARSAQETRA 321 Query: 281 -DVDNVYPVHRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREI 339 D P ++GT +D F+GSCTN R DL+ AA ++ RR+ E VR +V P S + Sbjct: 322 LDYMRAQPGKPMQGTPVDVVFIGSCTNSRLSDLREAAAILRGRRIAEGVRMLVVPGSEAV 381 Query: 340 YLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASS 399 A +G+ + F AGA PGC C+ + + PG++ ++T+NRNF GR G A + Sbjct: 382 RRDAEREGLHQVFTAAGAEWRVPGCSMCIAMNGDLAQPGQLVVSTSNRNFEGRQGKGART 441 Query: 400 VYLANPAVVAESAIEGVISAPQQ 422 V LA+PA A SA+ G I+ P++ Sbjct: 442 V-LASPATAAASALAGSIADPRE 463 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: 519 Number of extensions: 23 Number of successful extensions: 2 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: 471 Length adjustment: 33 Effective length of query: 395 Effective length of database: 438 Effective search space: 173010 Effective search space used: 173010 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