Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate AZOBR_RS04265 AZOBR_RS04265 2-isopropylmalate synthase
Query= curated2:Q8TYB1 (499 letters) >FitnessBrowser__azobra:AZOBR_RS04265 Length = 534 Score = 229 bits (583), Expect = 2e-64 Identities = 167/518 (32%), Positives = 258/518 (49%), Gaps = 36/518 (6%) Query: 3 DRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGE---FEAVR 59 +R+ ++DTTLRDG QT V +V +K+ IAR LD G+D +E G+P A+ + F Sbjct: 4 ERIYLYDTTLRDGAQTQDVDFSVADKIAIARDLDRLGIDYVEGGWPGANPTDDQFFAEAP 63 Query: 60 AIAGEELDA----EICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEAL 115 +A A G + + A I + V + T D H+ L + REE + Sbjct: 64 DLARSTFTAFGMTRRPGRSTANDPQLAALIQSKARAVCIVGKTWDFHVDVALAIPREENI 123 Query: 116 ERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMT 172 E + + F AE D + + Y KA EAGA V + DT G Sbjct: 124 ELIADSIAALKAAKGEALFDAEHFFDGYKRNPAYAASCIKAAYEAGARWVVLCDTNGGTL 183 Query: 173 PPEMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAG 229 P E+ + +V+D +P + +HCHND AVANSLAAV AG V T+NG+GER G Sbjct: 184 PHEIDEIVRQVIDEHGIPGDRLGIHCHNDTENAVANSLAAVRAGVRMVQGTINGLGERCG 243 Query: 230 NASLEQVVMALKALYDIELDVRTE---MLVELSRLVERLTGVVVPPNTPIVGENAFAHES 286 NA+L ++ +L ++ ++ +L E+SR + + P VG +AFAH+ Sbjct: 244 NANLVSLIPSLMLKMGCDVGIKPADLPLLTEISRKFDERLNRAPNRHAPYVGASAFAHKG 303 Query: 287 GIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEV--TEEQLDEI 344 G+H V K +YE + PE VG+RR+IV+ AGR + +L EMG+ V +E+L+ + Sbjct: 304 GLHVSAVEKDPSSYEHVEPEAVGNRRQIVMSDQAGRSNVIARLREMGMAVDPKDERLNRL 363 Query: 345 VRRVKELGDKGKR--VTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFT------- 395 + VK+ +G E E + R +GEVP+ L+ V ++ Sbjct: 364 LDIVKQRDTEGYAYDTAEASFELLVRRELGEVPD---YFTLKRFHVTDERRYNAKGELVV 420 Query: 396 -PTASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEELGM---DVELKEYRLE--AITG 449 A VRV + G+E+ ++G G V+A A+R+A+E L V+L +YR+ A Sbjct: 421 ESEAVVRVKIGGKEYHEVASGNGPVNALDTAMRKALEPLYPLLDGVKLSDYRVRILAAKD 480 Query: 450 GTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFV 487 GT A+ V +R + DG + G + +I+ AS++A V Sbjct: 481 GTGAMPRVLIRSRNGDGQEWSTLGVSTNIIEASMEALV 518 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: 560 Number of extensions: 28 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: 534 Length adjustment: 35 Effective length of query: 464 Effective length of database: 499 Effective search space: 231536 Effective search space used: 231536 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