Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_321162844.1 H035_RS0104410 alpha-isopropylmalate synthase regulatory domain-containing protein
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000421465.1:WP_321162844.1 Length = 520 Score = 267 bits (683), Expect = 6e-76 Identities = 186/501 (37%), Positives = 265/501 (52%), Gaps = 17/501 (3%) Query: 4 RVRIFDTTLRDGEQTPGVSLTVEEKVEIARKL-DEFGVDTIEAGFPVASEGEFEAVRAI- 61 R+ I DTTLRDGEQT GVS + EEK+ IA+ L + VD IE S+ E EAV I Sbjct: 15 RIEIMDTTLRDGEQTQGVSFSPEEKISIAKALLERVRVDRIEIASARVSDREKEAVTQIN 74 Query: 62 -----AGEELDAEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALE 116 AG E+ G + +D ++ +++ S+ H R +L + E + Sbjct: 75 AWTREAGFSDRVEVLGFVDHTRS-VDWIMETGGGTINLLTKGSEKHCRTQLGKNLETHTQ 133 Query: 117 RAIEGVEYASDHGVTVEFSAEDATRTDRD---YLLEVYKATVEAGADRVNVPDTVGVMTP 173 +E V YA G+ V ED + RD Y+ + AG R +PDT+GVMTP Sbjct: 134 DILETVAYAHTKGLIVNVYLEDWSNGYRDSPQYVFALMDNLRGAGIQRFMLPDTLGVMTP 193 Query: 174 PEMYRLTAEV-VDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNAS 232 E+Y ++ V ++ H HND+G+A AN +AAV+AGA VH TVN +GERAGNAS Sbjct: 194 EEVYASIHDMCVRYPELHFEFHPHNDYGLATANVMAAVQAGAAGVHCTVNCLGERAGNAS 253 Query: 233 LEQVVMALKALYDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHG 292 L +VV+ LK +EL V LV +S +VER +G V N PIVG + F +GIH+ G Sbjct: 254 LAEVVVTLKDKLGVELTVNESQLVRISDMVERFSGKRVSANAPIVGADVFTQTAGIHADG 313 Query: 293 VIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLDEIVRRVKELG 352 K ++PE R LGK +G+ +++K LE +GIE+T EQ +++R+ LG Sbjct: 314 DHKGNLYQSRLKPERFSRVRSYALGKMSGKASLRKNLERLGIELTAEQERHVLKRIVSLG 373 Query: 353 DKGKRVTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTASVRVYLDGEEHEAA 412 D + +T DDL I DV+ ES ++L A+ +G TAS+RV + GE H AA Sbjct: 374 DSKQTITTDDLPFIIADVLES--ESYQHIRLLNYAITSGLDLESTASIRVAVRGEAHTAA 431 Query: 413 STGVGSVDAAIRALREAIEELGMDV-ELKEYRLEAITGG-TDALAEVTVRLEDEDGNVTT 470 G G DA I AL + + + L +Y + GG T+AL E + + E T Sbjct: 432 GKGNGGFDAFIDALNQVMAHYDYTLPPLLDYEVRIPKGGHTNALTECIISWDCEHRTRVT 491 Query: 471 ARGAAEDIVMASVKAFVRGVN 491 RG + V AS+ A ++ +N Sbjct: 492 -RGVHVNQVFASMLATLKLIN 511 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: 556 Number of extensions: 26 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: 499 Length of database: 520 Length adjustment: 34 Effective length of query: 465 Effective length of database: 486 Effective search space: 225990 Effective search space used: 225990 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