Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate YP_004140223.1 Mesci_1009 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_000185905.1:YP_004140223.1 Length = 469 Score = 203 bits (516), Expect = 1e-56 Identities = 150/439 (34%), Positives = 218/439 (49%), Gaps = 60/439 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNV---PANTIGAA-EFQR 85 +D + H+ TSP + F + G R PE+ + V DHNV P G E R Sbjct: 29 IDRHLVHEVTSP---QAFEGLRMTGRKVR--HPEKTLAVVDHNVSTSPERKFGIKNEESR 83 Query: 86 VTREF----AREQGIVNIFQN--AAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAF 139 + E A++ G+ +N GI H + PE+GF PGM IV DSHT T+GAFGA Sbjct: 84 IQVEALAKNAKDFGVEYYSENDIRQGIVHIIGPEQGFTLPGMTIVCGDSHTSTHGAFGAL 143 Query: 140 ATGMGATDMAMVFATGKTWFMVPEAMRIEVTGE-PEGHVYAKDVILHIIGEIGVDGATYR 198 A G+G +++ V AT + M + V G+ PEG V AKD+IL IIGEIG G T Sbjct: 144 AHGIGTSEVEHVLATQTLIQRKAKNMLVRVDGQLPEG-VTAKDIILAIIGEIGTAGGTGY 202 Query: 199 SVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYV----RARTG------- 247 +E+ G+ I ++ + GRMTICNM++E GA+ G++ + T YV RA G Sbjct: 203 VIEYAGEAIRALSMEGRMTICNMSIEGGARAGLIAADETTFAYVKDKPRAPKGAAWDAAL 262 Query: 248 REFRVYSSDEDSQYLEDHHFDVSDLEPQVAC----------------PDDVDN------- 284 ++ SDE + + + D + L P V+ PDD+ + Sbjct: 263 EYWKTLQSDEGAHFDKVIVLDAAKLPPIVSWGSSPEDVVSVQGIVPNPDDITDENKRTSK 322 Query: 285 --------VYPVHRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPAS 336 + P R+ +D F+GSCTNGR EDL+ A+V+ + V V ++ P S Sbjct: 323 QRALDYMGLTPGTRITDITLDRVFIGSCTNGRIEDLRAVAKVVEGKTVSPHVDAMIVPGS 382 Query: 337 REIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDP 396 + +A +G+ + F+ AG PGC CL + L P E +T+NRNF GR G Sbjct: 383 GLVKEQAEAEGLDKIFVAAGFDWREPGCSMCLAMNDDRLKPHERCASTSNRNFEGRQGFK 442 Query: 397 ASSVYLANPAVVAESAIEG 415 + +L +PA+ A +AI G Sbjct: 443 GRT-HLVSPAMAAAAAIAG 460 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: 525 Number of extensions: 24 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: 428 Length of database: 469 Length adjustment: 33 Effective length of query: 395 Effective length of database: 436 Effective search space: 172220 Effective search space used: 172220 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 10 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