Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_051463020.1 HALAL_RS0116090 citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000527155.1:WP_051463020.1 Length = 512 Score = 190 bits (483), Expect = 9e-53 Identities = 153/508 (30%), Positives = 248/508 (48%), Gaps = 46/508 (9%) Query: 20 GVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIAGEELD-----------A 68 G+ +V +K+ +AR +DE GVD IE G+P A + E A EE++ Sbjct: 3 GLRYSVADKMSVARLIDELGVDYIEGGWPGALPSDTEFFER-ASEEINFKHAKLVAFGMT 61 Query: 69 EICGLARCVKGDIDAAIDADVDCVHVFIATSDI-HLRYKLEMSREEALERAIEGVEYASD 127 G+A + A ID+ + +A SDI H+R+ L+ S E LE + + Y + Sbjct: 62 RRAGIAAADDEGLGALIDSRAPTL-CLVAKSDIRHVRHALKASPAENLEMIRDSISYGRE 120 Query: 128 HGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPPEMYRLT---- 180 + V E D R DY V K++ +AGAD V + DT G P ++ R+ Sbjct: 121 YDREVFIDCEHFFDGFRHSPDYATTVVKSSFDAGADVVVLCDTNGGSIPSDIARIIGDLR 180 Query: 181 ---AEVVDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNASLEQVV 237 A+ + D+ + +H ND G AVAN+L AVE+G V T NG GER GNA + V+ Sbjct: 181 SRLADTMRPEDIRLGIHAQNDTGCAVANTLTAVESGVMHVQGTANGYGERPGNADIFSVI 240 Query: 238 MALKALYDIEL--DVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHGVIK 295 L+ + + E + S + + + + P VG AFAH++G+H+ + Sbjct: 241 GGLQTKMGMRVLPPGGLEKMTHTSHSIAAIANMPPNEHAPYVGHAAFAHKAGLHASAIKT 300 Query: 296 KAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEV--TEEQLDEIVRRVKELGD 353 Y I P+ VG+ RI++ + AGR +I+ K ++GIE+ ++ LD + +RVK+L Sbjct: 301 DPGLYNHIDPQVVGNDMRILVTEMAGRASIELKSRDLGIELRGQKDVLDRVTKRVKDLEA 360 Query: 354 KG--KRVTEDDLEAIARDVVGEVPESEAAVKLEEIAV-------MTGNKFTPTASVRVYL 404 +G + E + D E+P++ V+ +A A+VR+ + Sbjct: 361 QGWSFEAADASFELLLDD---ELPQANRVVRPFTVASYRVIIDHTRDGSVVCEATVRLEV 417 Query: 405 DGEEHEAASTGVGSVDAAIRALREAIEEL--GM-DVELKEYRLEAITG--GTDALAEVTV 459 DGE+ + G V+A ALR+A+ E G+ ++ L +Y++ + G GT+A+ V Sbjct: 418 DGEQTITTAQARGPVNALDAALRQALAERFPGLSEINLSDYKVRILAGTSGTEAITRVLT 477 Query: 460 RLEDEDGNVTTARGAAEDIVMASVKAFV 487 L D D TT G ++IV AS +A + Sbjct: 478 TLSDGDDEWTTV-GVDDNIVEASWRALI 504 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: 534 Number of extensions: 27 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: 512 Length adjustment: 34 Effective length of query: 465 Effective length of database: 478 Effective search space: 222270 Effective search space used: 222270 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 10 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