Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_011840981.1 RSPH17029_RS06990 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000015985.1:WP_011840981.1 Length = 550 Score = 218 bits (555), Expect = 4e-61 Identities = 173/534 (32%), Positives = 267/534 (50%), Gaps = 39/534 (7%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIA 62 +R+ I+DTTLRDG+QT GV + EK +IA LD GVD IE G+P A+ + E A+ Sbjct: 13 ERLWIYDTTLRDGQQTQGVQFSTPEKRQIAEALDRLGVDYIEGGWPGANPTDSEFFAALP 72 Query: 63 GEELDAEICGL----ARCVKGD--IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALE 116 G+ R + D + A +DA D V + T + H+ L ++ EE LE Sbjct: 73 AVRARVAAFGMTKRAGRSAENDDVLAAVLDAGTDTVCLVGKTHEFHVTTALGVTLEENLE 132 Query: 117 RAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTP 173 V + G AE D R + Y L +A + AGA V + DT G P Sbjct: 133 AIRASVAHVVARGREAILDAEHFFDGYRANPAYALGCLQAALGAGARWVVLCDTNGGTLP 192 Query: 174 PEMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGN 230 E+ R+ AEV+ A VP + +H H+D G AVA +LAAV+AGA QV T+NG+GER GN Sbjct: 193 AEVGRIVAEVI-AAGVPGDRLGIHTHDDTGTAVAATLAAVDAGARQVQGTLNGLGERCGN 251 Query: 231 ASLEQVV--MALKALYDIELDVRTEM-----LVELSRLVERLTGVVVPPNTPIVGENAFA 283 A+L ++ LK Y + + +V +SR+++ + V + VG +AFA Sbjct: 252 ANLTTLIPTFLLKEPYASRFETGIDREALSGMVRVSRMLDDILNRVPRRASAYVGASAFA 311 Query: 284 HESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVT--EEQL 341 H++G+H+ ++K TYE + P VG+ R I + AG+ ++ +L E G+EV + +L Sbjct: 312 HKAGLHASAILKDPATYEHVDPALVGNVRVIPMSNQAGQSNLRARLAEAGLEVPSGDPRL 371 Query: 342 DEIVRRVKELGDKGKRV--TEDDLEAIARDVVGEVPE----SEAAVKLEEIAVMTGNKFT 395 I+ VK D+G + E +AR +G +P V +E V G Sbjct: 372 GRILETVKAREDQGYAYDSAQASFELVARRELGLLPSFFEVKRYRVTVERRRVGEGTMTL 431 Query: 396 PTASVRVYLDGEEHEAASTGV---GSVDAAIRALREAI-EELGM------DVELKEYRLE 445 A V V +DG+ + S + G+ + AL +A+ ++LG D+ L ++++ Sbjct: 432 SEAVVVVLIDGQRVLSVSESLDENGTERGPVNALSKALAKDLGRWQSVIDDMRLVDFKVR 491 Query: 446 AITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGVN-RLARRRR 498 GGT+A V + ED G + G + +IV AS +A + +N +L R R Sbjct: 492 ITQGGTEAATRVIIDSEDGQGRRWSTVGVSPNIVDASFEALLDAINWKLVRDAR 545 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: 592 Number of extensions: 27 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: 550 Length adjustment: 35 Effective length of query: 464 Effective length of database: 515 Effective search space: 238960 Effective search space used: 238960 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 16 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