Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate Ac3H11_1525 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
Query= curated2:Q8TLF1 (424 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1525 Length = 473 Score = 237 bits (605), Expect = 5e-67 Identities = 157/448 (35%), Positives = 220/448 (49%), Gaps = 67/448 (14%) Query: 38 VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPAN-------------NETS 84 +D + H+ TS A +E KVW S IV DH P ++ Sbjct: 27 IDRHLVHEVTSPQAFEGLREAG-RKVWRMSSIVGTADHNTPTTGWEHGYDGITDPISKEQ 85 Query: 85 ATLQREIREWVKEQGIPNFYEVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFA 144 T + + F +GI H + PENG LPG VV DSH+ T+GAFGA A Sbjct: 86 ITTLNDNMATISPAAFFPFMHKRQGIVHVIGPENGATLPGMTVVCGDSHTSTHGAFGALA 145 Query: 145 TGVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAV 204 G+G +++ + AT L K ++ + V+G+L KGV KD+ L +IGK G AG T + Sbjct: 146 HGIGTSEVEHVMATQTLLAKKAKNMLVQVDGTLAKGVTPKDVVLAIIGKIGTAGGTGYTI 205 Query: 205 EFYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLKNR-----------AAAT 253 EF G R +++ GRMT+CNMAIE GA+ G+V D+KT E++K R A A Sbjct: 206 EFAGSVFRAMSMEGRMTVCNMAIEGGARAGLVAVDDKTIEYVKGRPLSPTGVEWDQAVAY 265 Query: 254 YEPVYADPDAVYLEEFTYDADDIEPQV---ACPHQVDNV--------------------- 289 ++ +++D DA + DA +I+PQV P V + Sbjct: 266 WKTLHSDADAQFDTVVKLDAAEIQPQVTWGTSPEMVLGIDARVPDPDKEKDANKRGAIER 325 Query: 290 ----------KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAAVLK--GKQVAVR---TIV 334 KP+ ++ +D+VFIG+CTN R+ED+ AAAV+K G++VA +V Sbjct: 326 ALTYMDLQPGKPINDIT---IDKVFIGSCTNSRIEDMREAAAVVKNLGRKVASNVKLALV 382 Query: 335 IPASRTTLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGR 394 +P S A G + AG PGC CL + L GE C ST+NRNF+GR Sbjct: 383 VPGSGLVKEQAEREGLDQIFKAAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGR 442 Query: 395 MGKGGFIYLASPATAAASALTGEITDPR 422 G GG +L SPA AAA+A+ G D R Sbjct: 443 QGAGGRTHLVSPAMAAAAAVHGHFVDIR 470 Lambda K H 0.318 0.135 0.400 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: 491 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 424 Length of database: 473 Length adjustment: 33 Effective length of query: 391 Effective length of database: 440 Effective search space: 172040 Effective search space used: 172040 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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