Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_007474786.1 CMTB2_RS06170 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_000170735.1:WP_007474786.1 Length = 425 Score = 384 bits (987), Expect = e-111 Identities = 201/427 (47%), Positives = 284/427 (66%), Gaps = 13/427 (3%) Query: 4 MNMTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPE 63 M +TEKI A+ G REV PGEII VD+ + +D T+P +I+ FR+ G ++ P+ Sbjct: 3 MTITEKIFADHIG-REVKPGEIIMCDVDMTIGNDITTPISIKAFRE----SGAKKLAKPD 57 Query: 64 RIVMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIF-QNAAGICHQVLPERGFVRPGMV 122 +V DH +P I +A ++ REFA E + N F + GI H++LPE+G V PG V Sbjct: 58 NFAIVLDHFIPPKDIASANQAKINREFAYEHNLKNFFDEKDMGIEHRLLPEKGLVIPGDV 117 Query: 123 IVGADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDV 182 I+GADSHTCT+GA GAF+TGMG+TD+A TGK+WF VPE++++ TG+ HVY KD+ Sbjct: 118 IIGADSHTCTHGALGAFSTGMGSTDIAFSMITGKSWFKVPESIKVVFTGQRGEHVYGKDL 177 Query: 183 ILHIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQT---L 239 IL +I IGVDGA Y+++EFTGDTIE++ + RM++CNM +E GAKNGI+ ++ T L Sbjct: 178 ILELIRRIGVDGALYKALEFTGDTIENLPMDDRMSLCNMVIEAGAKNGIIAYDKITESFL 237 Query: 240 DYVRARTGREF--RVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRV--EGTH 295 + V+ +++ SD D++Y++ DV +LEP VA P N P+ + Sbjct: 238 EEVKKHNPLRSTPKIHYSDPDAKYVKIIEIDVDNLEPMVAYPYLPSNGKPISEAVKDDIE 297 Query: 296 IDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRA 355 I + ++GSCTNG DL+ AA ++ +RVH+ VR IV+PA++ IY +A +GII+T I A Sbjct: 298 IHQVYIGSCTNGTLSDLRTAANILKGKRVHKRVRLIVTPATQRIYKQAEHEGIIDTLIDA 357 Query: 356 GAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEG 415 GA+V NP CG CLG +MG+L GE +ATTNRNFRGRMG +S +YL+N AV A SAI G Sbjct: 358 GAVVANPTCGACLGGYMGILGDGERCVATTNRNFRGRMGSRSSEIYLSNSAVAAASAIAG 417 Query: 416 VISAPQQ 422 I+ P++ Sbjct: 418 KIADPRE 424 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: 509 Number of extensions: 25 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 396 Effective length of database: 393 Effective search space: 155628 Effective search space used: 155628 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