Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_084274801.1 B8779_RS01390 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_900176045.1:WP_084274801.1 Length = 421 Score = 377 bits (968), Expect = e-109 Identities = 195/421 (46%), Positives = 280/421 (66%), Gaps = 9/421 (2%) Query: 6 MTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERI 65 +TEKI +E G REV GEI+E +D+ + +D T+P +I+ FR+ G ++ P+ Sbjct: 5 ITEKIFSEHVG-REVKAGEIVECELDMIIGNDITTPISIKAFRE----SGAKKLAKPDNF 59 Query: 66 VMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIF-QNAAGICHQVLPERGFVRPGMVIV 124 +V DH +PA I +A +++REFA E + + F + GI H +LPE+G V PG VI+ Sbjct: 60 AIVLDHFIPAKDIASANQAKISREFAYEHNLKHFFDEKDMGIEHALLPEKGLVVPGDVII 119 Query: 125 GADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVIL 184 GADSHTCT+GA GAFATGMG+TD+A TGK WF VP ++++ TG+ + +VY KD+IL Sbjct: 120 GADSHTCTHGALGAFATGMGSTDLAYGMITGKNWFKVPPSIKVVYTGKLDEYVYGKDLIL 179 Query: 185 HIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRA 244 +I IGVDGA Y+++EFTGDTIE++D+ GR ++CNMA+E GAKNGI+ + T ++ Sbjct: 180 ELIRRIGVDGALYKALEFTGDTIENLDMDGRFSLCNMAIEAGAKNGIIAVDEITKAFLAD 239 Query: 245 R-TGREFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVE--GTHIDEAFL 301 + RE +++ SDED++Y + DV+ LEP +A P N P+ +D+ F+ Sbjct: 240 KDLAREPKIHYSDEDAEYEQVIEIDVNSLEPVIAFPHLPSNGRPISEAAKMDLKVDQVFI 299 Query: 302 GSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVCN 361 GSCTNGR D+ IAAE++ R+V R IV+PA+++I +A + G I+ I AGA+V N Sbjct: 300 GSCTNGRLSDIAIAAEILKGRKVARHTRMIVTPATQKILKEAEKQGYIDILIDAGAVVSN 359 Query: 362 PGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAPQ 421 P CG CLG +MG+LA E ++TTNRNF GRMG S +YLAN AV A SA+ G I+ P+ Sbjct: 360 PTCGACLGGYMGILADNERCVSTTNRNFIGRMGARTSEIYLANSAVAAASAVAGKIADPR 419 Query: 422 Q 422 + Sbjct: 420 E 420 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: 482 Number of extensions: 24 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: 421 Length adjustment: 32 Effective length of query: 396 Effective length of database: 389 Effective search space: 154044 Effective search space used: 154044 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 Jul 25 2024. The underlying query database was built on Jul 25 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