Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate SMc02546 SMc02546 alpha-isopropylmalate/homocitrate synthase family transferase
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__Smeli:SMc02546 Length = 538 Score = 244 bits (623), Expect = 5e-69 Identities = 172/531 (32%), Positives = 270/531 (50%), Gaps = 38/531 (7%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62 +R+ +FDTTLRDG+QTPG+ +VE+K+ IA LD+FG+D +E G+P A+ + E + Sbjct: 4 ERIYLFDTTLRDGQQTPGIDFSVEDKIAIASLLDQFGMDYVEGGYPGANPTDTEFFKCRR 63 Query: 63 GEELD------AEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALE 116 ++ + G++ + A + A D + + + D H+ L + EE L+ Sbjct: 64 TDKASFVAFGMTKRAGVSASNDPGLSALLSAKSDAICLVAKSWDYHVEVALGCTNEENLD 123 Query: 117 RAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTP 173 VE G E D + + Y L K EAGA V + DT G P Sbjct: 124 NIRASVEAVVASGREAMVDCEHFFDGYKANSAYALACAKTAFEAGARWVVLCDTNGGTQP 183 Query: 174 PEMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGN 230 PE+ + + V+ A VP + +H HND G AVANSLAAVEAG Q+ T+NGIGER GN Sbjct: 184 PEIREIVSAVI-AEGVPGANLGIHAHNDTGQAVANSLAAVEAGVRQIQGTLNGIGERCGN 242 Query: 231 ASLEQVV--MALKALYD--IELDVRTEMLVELSRLV---ERLTGVVVPPNTPIVGENAFA 283 A+L ++ +ALK Y E + E L EL++L + L P P VG +AFA Sbjct: 243 ANLVTLIATLALKETYSSRFETGIDAERLQELTKLAHAFDELLNRSPDPQAPYVGASAFA 302 Query: 284 HESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEE--QL 341 ++GIH+ ++K TYE + PE VG+ R++++ G+ L+ GI V+++ +L Sbjct: 303 TKAGIHASALLKDPRTYEHVAPESVGNLRKVMVSDQGGKANFINALKRRGITVSKDDPRL 362 Query: 342 DEIVRRVKELGDKGKRVTEDD--LEAIARDVVGEVPESEAAVKLEEIAVMTGNKF----- 394 D+++ VKE G D +A ++G VP+ ++E VM +F Sbjct: 363 DKLISIVKEREATGYAYEGADASFALLASRILGTVPD---FFRVESFRVMVERRFDANGK 419 Query: 395 ---TPTASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEELG---MDVELKEYRLEAIT 448 A VRV +DGE + + G G V+A ALR+ + + D+EL +Y++ + Sbjct: 420 LKTVSEAVVRVIVDGETMMSVAEGHGPVNALDLALRKDLGKYQSEIADLELADYKVRILN 479 Query: 449 GGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGVNRLARRRRD 499 GGT+A+ V + D G G +++I+ AS +A + + + RD Sbjct: 480 GGTEAVTRVLIESTDRSGARWWTVGVSDNIIDASFQALMDSIVYKLLKNRD 530 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: 517 Number of extensions: 16 Number of successful extensions: 6 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: 538 Length adjustment: 35 Effective length of query: 464 Effective length of database: 503 Effective search space: 233392 Effective search space used: 233392 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 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