Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_020565007.1 A3OW_RS0118785 alpha-isopropylmalate synthase regulatory domain-containing protein
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000372865.1:WP_020565007.1 Length = 514 Score = 245 bits (625), Expect = 3e-69 Identities = 167/500 (33%), Positives = 261/500 (52%), Gaps = 17/500 (3%) Query: 5 VRIFDTTLRDGEQTPGVSLTVEEKVEIARKL-DEFGVDTIEAGFPVASEGEFEAVRAI-- 61 +++ DTTLRDGEQT GVS T EKV IA+ L VD IE S GE EAV I Sbjct: 8 IQLMDTTLRDGEQTQGVSFTPAEKVNIAKALLQSLRVDRIEVASARVSAGEKEAVTNINQ 67 Query: 62 ----AGEELDAEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALER 117 G + E+ G + +D ++ +++ S+ H R +L +RE+ Sbjct: 68 WAKQEGFDGCVEVLGFVDHTRS-VDWILETGGSVINLLTKGSEKHCREQLGKTREQHTAD 126 Query: 118 AIEGVEYASDHGVTVEFSAEDAT---RTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPP 174 ++ V+YA + V ED + + DY+ + + EAG +PDT+GVM+P Sbjct: 127 ILQTVDYALSRSLKVNVYLEDWSNGYQNSPDYVYALMDSLKEAGISHFMLPDTLGVMSPD 186 Query: 175 EMYRLTAEVVDAVD-VPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNASL 233 E++ +++ + H HND+G+A AN +AAV AGA VH TVN +GERAGNASL Sbjct: 187 EVFTSFSDMCRCYPALQFDFHPHNDYGLATANVMAAVRAGATAVHCTVNCLGERAGNASL 246 Query: 234 EQVVMALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHGV 293 +V + L+ +++L + +V LS +VE +G V N PIVG + F +GIH+ G Sbjct: 247 AEVAVVLRDKMNMQLSIDETHIVRLSNMVENFSGKRVAANAPIVGSDVFTQTAGIHADGD 306 Query: 294 IKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLDEIVRRVKELGD 353 K + PE R LGK +G+ ++KK LE + I+++EE +++ R+ LGD Sbjct: 307 HKGGLYKSRLSPERFSRSRSYALGKMSGKASLKKNLELLEIDLSEENQKKVLARIVSLGD 366 Query: 354 KGKRVTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTASVRVYLDGEEHEAAS 413 + +T DDL I DV+ ++ +KL + +G TAS+R+ ++G +H + Sbjct: 367 SKQTITTDDLPFIIADVLES--KNYQHIKLLNCFITSGLHLESTASLRLDVNGAKHVISG 424 Query: 414 TGVGSVDAAIRALREAIEELGMDV-ELKEYRLEAITGG-TDALAEVTVRLEDEDGNVTTA 471 G G DA I A+ +A++E V L +Y + GG TDAL E + + + Sbjct: 425 AGNGGFDAFIDAVNKAMKEHDYTVPPLADYEVRIPKGGHTDALTECVITW-NCGSELRKT 483 Query: 472 RGAAEDIVMASVKAFVRGVN 491 RG + V A++ A ++ +N Sbjct: 484 RGVHANQVFAAIMATLKIIN 503 Lambda K H 0.315 0.133 0.364 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: 480 Number of extensions: 20 Number of successful extensions: 5 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: 499 Length of database: 514 Length adjustment: 34 Effective length of query: 465 Effective length of database: 480 Effective search space: 223200 Effective search space used: 223200 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 (21.5 bits) S2: 52 (24.6 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