Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF1877 HP15_1834 protein containing 3-isopropylmalate dehydratase, large subunit region domain
Query= curated2:Q8TLF1 (424 letters) >FitnessBrowser__Marino:GFF1877 Length = 472 Score = 236 bits (601), Expect = 1e-66 Identities = 152/442 (34%), Positives = 225/442 (50%), Gaps = 58/442 (13%) Query: 38 VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPANNE----------TSATL 87 +D + H+ TS A + + K W + DH P + S Sbjct: 28 IDRQLLHEVTSPQAFEGLR-LAGRKPWRIDANIATPDHNVPTTDRDRGVEGIVDPVSRIQ 86 Query: 88 QREIREWVKEQGIPNFY--EVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFAT 145 + + E GI F + +GI H + PE G LPG +V DSH+ T+GAFG A Sbjct: 87 VETLDKNCDEFGILEFKIKDQRQGIVHVIGPEQGATLPGMSIVCGDSHTSTHGAFGCLAH 146 Query: 146 GVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAVE 205 G+G +++ + AT L + ++ + V G L GV KD+ L +IGK G AG T A+E Sbjct: 147 GIGTSEVEHVLATQCLVQQKMKNMLVKVNGKLGPGVTGKDVVLAIIGKIGTAGGTGHAIE 206 Query: 206 FYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLKNR-----------AAATY 254 F G+AIR L++ GRMT+CNM+IE GA+ G+V D+ T E+++NR A + Sbjct: 207 FGGEAIRGLSMEGRMTICNMSIEAGARVGMVAVDDTTIEYVRNRPFGPKGEQWDAAVEYW 266 Query: 255 EPVYADPDAVYLEEFTYDADDIEPQVAC-----------------PHQVDNVKPVGEVEG 297 +++D DAV+ + + +I+PQV+ + D +K G V Sbjct: 267 RTLHSDSDAVFDKIVELEGSEIQPQVSWGTSPEMVAGIDGKVPDPEQEADPIKREGIVRA 326 Query: 298 --------------THVDQVFIGTCTNGRLEDLEVAAAVLKGKQVA---VRTIVIPASRT 340 +D+VFIG+CTN R+EDL AAAV+KG++V+ + +V+P S Sbjct: 327 LKYMGLQPNMAITDIKLDRVFIGSCTNSRIEDLREAAAVVKGRKVSPILKQAMVVPGSGL 386 Query: 341 TLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKGGF 400 A + G + ++AG+ PGC CL + LG+GE C ST+NRNF+GR G GG Sbjct: 387 VKAQAEQEGLDKIFIEAGLEWRDPGCSMCLAMNADKLGQGEHCASTSNRNFEGRQGFGGR 446 Query: 401 IYLASPATAAASALTGEITDPR 422 +L SPA AAA+A+TG D R Sbjct: 447 THLVSPAMAAAAAVTGHFVDVR 468 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: 503 Number of extensions: 26 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: 424 Length of database: 472 Length adjustment: 33 Effective length of query: 391 Effective length of database: 439 Effective search space: 171649 Effective search space used: 171649 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