Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate 8499505 DvMF_0275 putative alpha-isopropylmalate/homocitrate synthase family transferase (RefSeq)
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__Miya:8499505 Length = 540 Score = 201 bits (511), Expect = 5e-56 Identities = 158/526 (30%), Positives = 255/526 (48%), Gaps = 40/526 (7%) Query: 1 MPDRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRA 60 M R++++DTTLRDG Q+ ++LT +K++IA KLDE G+D IE G+P ++ + + Sbjct: 1 MTRRIQLYDTTLRDGSQSEDINLTAADKLKIALKLDEIGIDRIEGGWPGSNPVDVAFFKE 60 Query: 61 IAGEELD-AEICGLARCVKGDIDAAIDADVDCV--------HVFIATSDIHLRYKLEMSR 111 IA L A I + A D ++ + +F + ++H L + Sbjct: 61 IANYHLKHAVISAFGSTHHPNFTADSDPNLRAIAESGARVASIFGKSCEVHAAEALRLDA 120 Query: 112 EEALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTV 168 LE + V + V F AE D R + Y L + EAGAD + + DT Sbjct: 121 ARNLEIIGDSVAFLKGKLAEVYFDAEHFFDGYRHNAAYALSALRRAHEAGADVLVLCDTN 180 Query: 169 GVMTPPEMYRLTAEVVDAVD-VPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGER 227 G P E+ R+ EV +A+ V +H HND +AVANS+AAV+AGA Q+ T+NG+GER Sbjct: 181 GGTLPHEVARIVTEVREALPGAAVGIHAHNDCELAVANSIAAVQAGAVQIQGTINGVGER 240 Query: 228 AGNASLEQVVMALKALYDIEL----DVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFA 283 GNA+L ++ L+ + E + R + L ++ V + + P VG +AFA Sbjct: 241 CGNANLCSIIPTLELKFGGEYTCLPEGRLQQLTAVAAYVSEVANIPPFSRQPYVGRSAFA 300 Query: 284 HESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQ--- 340 H+ G+H V +K+ YE I P+ VG+R+RI++ + AGR I G + +++ Sbjct: 301 HKGGVHVSAVNRKSSLYEHISPDVVGNRQRILITELAGRSNIVSLARRFGFHLDKDEPVV 360 Query: 341 ---LDEIVRRVKELGDKGKRVTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPT 397 L E+ ++ D +L + + V E ++ + ++ P Sbjct: 361 KGLLTELKKKASLGYDYAAAEASVELLILRKLARRGVREFFRLLQFRVLETKHDSEGEPV 420 Query: 398 ASVRVYLDGE---EHEAASTGVGSVDAAIRALREAIEELGM-----DVELKEYRLEAIT- 448 + V V +D E EH AA TG G V+A ALR+A+ LG ++ L ++++ +T Sbjct: 421 SEVSVMVDVEGVTEHTAA-TGRGPVNALDNALRKAL--LGFYPRLSEMRLLDFKVRVLTG 477 Query: 449 ----GGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490 GGT + V + D D T G + +I+ AS +A V Sbjct: 478 AETGGGTASTVRVLIESGDSDSRWVTV-GVSFNIIEASWQALADSV 522 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: 584 Number of extensions: 25 Number of successful extensions: 3 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: 540 Length adjustment: 35 Effective length of query: 464 Effective length of database: 505 Effective search space: 234320 Effective search space used: 234320 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