Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 14218 b0072 isopropylmalate isomerase large subunit (NCBI)
Query= curated2:Q8TLF1 (424 letters) >FitnessBrowser__Keio:14218 Length = 466 Score = 262 bits (670), Expect = 1e-74 Identities = 171/465 (36%), Positives = 242/465 (52%), Gaps = 57/465 (12%) Query: 14 TISEKIFSRAAGTEAKANDFVLADVDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPF 73 T+ EK+F EA+ N+ L +D + H+ TS A + + V P + Sbjct: 4 TLYEKLFDAHVVYEAE-NETPLLYIDRHLVHEVTSPQAFDGLRA-HGRPVRQPGKTFATM 61 Query: 74 DHIAP-------ANNETSATLQREIREWVKEQGIPNFYEVG---EGICHQVLPENGFALP 123 DH A E + +E+ + KE G+ Y++ +GI H + PE G LP Sbjct: 62 DHNVSTQTKDINACGEMARIQMQELIKNCKEFGV-ELYDLNHPYQGIVHVMGPEQGVTLP 120 Query: 124 GKLVVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYA 183 G +V DSH+ T+GAFGA A G+G +++ + AT L ++ ++ V+G G+ A Sbjct: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180 Query: 184 KDLTLYLIGKTGIAGATYKAVEFYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTF 243 KD+ L +IGKTG AG T VEF G+AIR+L++ GRMTLCNMAIEMGAK G+V PDE TF Sbjct: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240 Query: 244 EFLKNR-----------AAATYEPVYADPDAVYLEEFTYDADDIEPQVAC---PHQV--- 286 ++K R A A ++ + D A + T A++I PQV P QV Sbjct: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300 Query: 287 -DNV------------------------KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAA 321 DN+ KP + +D+VFIG+CTN R+EDL AA Sbjct: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 Query: 322 VLKGKQVA--VRTIVIPASRTTLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGE 379 + KG++VA V+ +V+P S A G + ++AG PGC CL + L Sbjct: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420 Query: 380 GEVCVSTANRNFKGRMGKGGFIYLASPATAAASALTGEITDPRTV 424 GE C ST+NRNF+GR G+GG +L SPA AAA+A+TG D R + Sbjct: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 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: 507 Number of extensions: 22 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: 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