Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate PfGW456L13_3592 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
Query= curated2:O27668 (428 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 Length = 473 Score = 211 bits (537), Expect = 4e-59 Identities = 145/440 (32%), Positives = 213/440 (48%), Gaps = 62/440 (14%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDH---NVPANTIGAAE---- 82 +D + ++ TSP R+ + W P + V DH VP T + Sbjct: 30 IDRQVANEYTSPQAFSGMREAGRKA-----WRPGATLAVVDHVNPTVPTRTAAMPDAGGA 84 Query: 83 -----FQRVTREFAREQGIVNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFG 137 F+ R+F E + ++ GI H V PE+GF+ PGMV+ DSHT TYGA G Sbjct: 85 RQVSYFEENCRDFGIE--LFDVLDKRQGIEHVVAPEQGFILPGMVVAAGDSHTTTYGALG 142 Query: 138 AFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATY 197 AF G+G +++ + A+ + + MR+ V G V +KD+I+ +I +IG GAT Sbjct: 143 AFGFGIGTSEIEHLLASQTLVYKRLKTMRVTVNGVLGTGVTSKDIIMALIEKIGASGATG 202 Query: 198 RSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYV----RARTGR----- 248 ++EF G I + V RMTICNMAVE GA+ M P+ + Y+ RA G+ Sbjct: 203 YAIEFAGPAISDLSVEARMTICNMAVEAGARGAFMAPDDKVFAYLQHKPRAPQGQLWEQA 262 Query: 249 --EFRVYSSDEDSQYLEDHHFDVSDLEPQV---ACPDDVDNV------------------ 285 ++R SDE + + + DV+ LEP V PD +V Sbjct: 263 VAKWRGLHSDEGAVFDREVTLDVAALEPMVTWGTSPDQAASVGGHVPDPAAQPDLILRQG 322 Query: 286 ----------YPVHRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPA 335 P + I AF+GSCTN R EDL+ A V+ +RV VR ++ P Sbjct: 323 MQRALNYMGLTPGMPLSDVVISHAFIGSCTNARIEDLRDVARVVRGKRVASHVRAMIVPG 382 Query: 336 SREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGD 395 S + +A ++G+ + F+ AG GC CL + VLAPG+ ++TNRNF GR G Sbjct: 383 STLVRHQAEDEGLAQIFLDAGFEWRQSGCSMCLAMNDDVLAPGDRCASSTNRNFEGRQGA 442 Query: 396 PASSVYLANPAVVAESAIEG 415 A + +L +PA+VA +AI G Sbjct: 443 GART-HLMSPAMVAAAAITG 461 Lambda K H 0.320 0.137 0.408 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: 533 Number of extensions: 23 Number of successful extensions: 2 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: 428 Length of database: 473 Length adjustment: 33 Effective length of query: 395 Effective length of database: 440 Effective search space: 173800 Effective search space used: 173800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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