Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate RR42_RS14400 RR42_RS14400 isopropylmalate isomerase
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__Cup4G11:RR42_RS14400 Length = 469 Score = 218 bits (556), Expect = 2e-61 Identities = 147/445 (33%), Positives = 216/445 (48%), Gaps = 61/445 (13%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPANTETSA-----------T 53 +D + H+ TS A K + VW S + DH P + T Sbjct: 27 IDRHLLHEVTSPQAFEGLK-LAQRPVWRISANLAVSDHNVPTTDRSQGIADPVSKLQVDT 85 Query: 54 LQKEIREWVREQSIPNFYEIGEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATG 113 L + Q N ++ +GI H + PE G LPG +V DSH+ T+GAFGA A G Sbjct: 86 LDNNCDAYGITQFKMN--DLRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALAHG 143 Query: 114 VGATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEF 173 +G +++ + AT L K ++ + VEG L + AKD+ L +IGK G AG T +EF Sbjct: 144 IGTSEVEHVLATQTLLGKKAKNMLVRVEGKLPRGCTAKDIVLAVIGKIGTAGGTGYTIEF 203 Query: 174 YGQAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNRAVAP-----------YE 222 G AI +LS+ GRMT+CNMAIE GA+ G+V D+ T +++K R +P + Sbjct: 204 AGSAIRDLSMEGRMTVCNMAIEAGARAGLVAVDDVTLEYVKGRPFSPQGVEWEQAVGYWR 263 Query: 223 PVYSDPDASYLKEFVYDAGDIEPQV---ACPHQVDNV----------------------- 256 ++SD A + + A D+ PQV P V ++ Sbjct: 264 TLHSDAGAHFDQVVELRAEDVRPQVTWGTSPEMVVSIEDRVPDPEKEKDPNKRNAMERAL 323 Query: 257 -----KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAASVLK--GKKVTVR---TIIIPASR 306 +P V+ +D+VFIG+CTN R+ED+ AA V++ G++V +++P S Sbjct: 324 EYMGLQPNVPVDSIKIDKVFIGSCTNSRIEDMRAAAWVVQKLGRRVASNVKLAMVVPGSG 383 Query: 307 STLLAAIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDG 366 A + G ++ AG PGC CL + L GE C ST+NRNF+GR G G Sbjct: 384 LVKEQAEREGLDKVFKAAGFEWREPGCSMCLAMNADRLEAGERCASTSNRNFEGRQGAGG 443 Query: 367 FIYLASPATAAASALTGEITDPRKI 391 +L SPA AAA+A+ G D R++ Sbjct: 444 RTHLVSPAMAAAAAIEGHFVDIRQL 468 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: 425 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 391 Length of database: 469 Length adjustment: 32 Effective length of query: 359 Effective length of database: 437 Effective search space: 156883 Effective search space used: 156883 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