Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_004512099.1 GMET_RS06385 3-isopropylmalate dehydratase large subunit
Query= curated2:Q8PZT3 (391 letters) >NCBI__GCF_000012925.1:WP_004512099.1 Length = 427 Score = 353 bits (906), Expect = e-102 Identities = 177/399 (44%), Positives = 252/399 (63%), Gaps = 13/399 (3%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPANTETSATLQKEIREWVRE 64 +D M H+ T+ +A+ +RV+DP++I DH+ P+ +AT K +R+W R Sbjct: 27 LDVVMCHEITTPIAIADLMARGKDRVFDPTKIKAVIDHVTPSKDSKTATQAKMLRDWARR 86 Query: 65 QSIPNFYEIGE-GICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVGATDMAEIF 123 +I +F+++G G+CH + PE G+ PG ++ DSH+CT+GAFGAFA GVG TD+ Sbjct: 87 HAIKDFFDVGHNGVCHALFPEKGYIRPGYTVIMGDSHTCTHGAFGAFAAGVGTTDLEVGI 146 Query: 124 ATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFYGQAISELSV 183 G F+ P+S R+ + G+L K VYAKD+ LY+IG+ G+ GAT + +EF G + +++ Sbjct: 147 LKGVCAFREPKSIRINLNGTLPKGVYAKDVILYVIGQLGVNGATDRVMEFRGPVVDAMTM 206 Query: 184 AGRMTLCNMAIEMGAKTGIVPPDEKTFDFL----------KNRAVAPYEPVYSDPDASYL 233 RMTLCNMAIE G +GI PD T ++L K A+A + SD DA Y Sbjct: 207 ESRMTLCNMAIEAGGTSGICMPDMVTVEYLWPFIENEYPSKEAALAEFSTWRSDDDAVYE 266 Query: 234 KEFVYDAGDIEPQVACPHQVDNVKPVGEVEGTHVDQVFIGTCTNGRLEDLEVAASVLKGK 293 + +D +EP V ++ D VKP+ E+ G+ VDQV++G+CTNGRLEDL +AA +LKGK Sbjct: 267 RVLDFDVSVLEPIVTFGYKPDQVKPISEIAGSPVDQVYLGSCTNGRLEDLRIAARILKGK 326 Query: 294 KV--TVRTIIIPASRSTLLAAIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCV 351 K+ +VR I+ PA+ A+ G ++I ++AG + P CG CLG GVL EGEVC Sbjct: 327 KIAPSVRGILSPATPKIYKDAMAEGLIDIFMEAGFCVTNPTCGACLGMSNGVLAEGEVCA 386 Query: 352 STANRNFKGRMGKDGFIYLASPATAAASALTGEITDPRK 390 ST NRNF GRMGK G ++L SPAT+AA+A+ G I DPRK Sbjct: 387 STTNRNFMGRMGKGGMVHLMSPATSAATAIEGVIADPRK 425 Lambda K H 0.318 0.135 0.401 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: 441 Number of extensions: 20 Number of successful extensions: 4 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: 391 Length of database: 427 Length adjustment: 31 Effective length of query: 360 Effective length of database: 396 Effective search space: 142560 Effective search space used: 142560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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