Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF2931 PGA1_c29780 3-isopropylmalate dehydratase large subunit
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__Phaeo:GFF2931 Length = 467 Score = 258 bits (659), Expect = 2e-73 Identities = 158/440 (35%), Positives = 231/440 (52%), Gaps = 54/440 (12%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPANTETSATLQKEIREWVRE 64 +D + H+ TS A + M +V P + + DH P + + ++ E E Sbjct: 28 IDRHLVHEVTSPQAFEGLR-MAGRKVHAPDKTIAVPDHNVPTTLDRAKGIENEESRIQVE 86 Query: 65 QSIPNFYEIG----------EGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGV 114 N E G +GI H V PE G+ LPG +V DSH+ T+GAFGA A G+ Sbjct: 87 ALDKNAREFGVHYYPVDDVRQGIVHIVGPEQGWTLPGMTVVCGDSHTATHGAFGALAHGI 146 Query: 115 GATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFY 174 G +++ + AT L K ++ ++ + G L V AKD+TL +IG+TG AG T +E+ Sbjct: 147 GTSEVEHVLATQTLIQKKSKNMKVEITGKLKPGVTAKDITLAVIGETGTAGGTGYVIEYC 206 Query: 175 GQAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNRAVAP-----------YEP 223 G+AI +L++ GRMT+CNMAIE GA+ G++ PDE TF+++K R AP ++ Sbjct: 207 GEAIRDLTMEGRMTVCNMAIEGGARAGLIAPDETTFEYVKGRPHAPKGAQWEAALNWWKT 266 Query: 224 VYSDPDASYLKEFVYDAGDIEPQVACPHQVDNVKPV------------GEVEGT------ 265 +++D A + K DI+P V ++V P+ G+VE Sbjct: 267 LFTDEGAHFDKVVTLKGEDIQPVVTWGTSPEDVLPITGVVPAPEDFTGGKVEAARRSLEY 326 Query: 266 ------------HVDQVFIGTCTNGRLEDLEVAASVLKGKKVT--VRTIIIPASRSTLLA 311 +D VFIG+CTNGR+EDL A V+KGKK+ +R +++P S Sbjct: 327 MGLTPGQKLTDIEIDTVFIGSCTNGRIEDLRAVAEVVKGKKIKDGMRAMVVPGSGLVRAQ 386 Query: 312 AIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLA 371 A + G EIL AG GC CL + L EGE C +T+NRNF+GR G G +L Sbjct: 387 AEEEGIAEILQDAGFEWRLAGCSMCLAMNPDQLSEGERCAATSNRNFEGRQGYKGRTHLV 446 Query: 372 SPATAAASALTGEITDPRKI 391 SPA AAA+ALTG++TD R++ Sbjct: 447 SPAMAAAAALTGKLTDVREL 466 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: 494 Number of extensions: 18 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: 391 Length of database: 467 Length adjustment: 32 Effective length of query: 359 Effective length of database: 435 Effective search space: 156165 Effective search space used: 156165 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: 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