Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate HSERO_RS16515 HSERO_RS16515 isopropylmalate isomerase
Query= curated2:Q8TLF1 (424 letters) >FitnessBrowser__HerbieS:HSERO_RS16515 Length = 466 Score = 231 bits (588), Expect = 5e-65 Identities = 156/441 (35%), Positives = 220/441 (49%), Gaps = 55/441 (12%) Query: 38 VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPANNETS------ATLQREI 91 +D + H+ TS A K + + W S ++ DH P + + LQ E Sbjct: 27 IDRHLLHEVTSPQAFEGLK-LAGRQPWRNSANLMVADHNVPTTDRAHGIADPISRLQVET 85 Query: 92 REW-VKEQGIPNF--YEVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFATGVG 148 + KE + F + +GI H + PE G LPG VV DSH+ T+GAF A A G+G Sbjct: 86 LDGNAKEYSLTYFGMNDKRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFAALAHGIG 145 Query: 149 ATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAVEFYG 208 +++ + AT L + ++ + V+G+L GV AKD+ L +IGK G AG T A+EF G Sbjct: 146 TSEVEHVLATQTLLARKSKAMLVQVDGALPAGVTAKDIVLAVIGKIGTAGGTGYAIEFAG 205 Query: 209 QAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLK-----------NRAAATYEPV 257 IR L++ GRMT+CNMAIE GA+ G+V D+ T E+LK RA + + + Sbjct: 206 STIRSLSMEGRMTVCNMAIEAGARAGMVAFDDTTLEYLKGRPFSPSGPHWERAVSYWRSL 265 Query: 258 YADPDAVYLEEFTYDADDIEPQV---ACPHQVDNV------------------------- 289 ++DP A + T +A +I+PQV P V V Sbjct: 266 HSDPGAKFDMVVTLNAAEIKPQVTWGTSPEMVVAVDARVPDPDKEKDPTKRDGMEKALAY 325 Query: 290 ---KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAAVLKGKQVAVR---TIVIPASRTTLL 343 KP +E +D+VFIG+CTN R+EDL AA V++GK A +V+P S Sbjct: 326 MALKPNTPIEDIRIDKVFIGSCTNSRIEDLREAAKVVRGKFRASNVKLAMVVPGSGLVKE 385 Query: 344 AAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKGGFIYL 403 A G + AG PGC CL + L GE C ST+NRNF+GR G GG +L Sbjct: 386 QAEREGLDKIFRDAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGRQGAGGRTHL 445 Query: 404 ASPATAAASALTGEITDPRTV 424 SPA AAA+ + G D R++ Sbjct: 446 VSPAMAAAAGIAGHFVDVRSL 466 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: 451 Number of extensions: 14 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: 466 Length adjustment: 32 Effective length of query: 392 Effective length of database: 434 Effective search space: 170128 Effective search space used: 170128 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