Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_013645928.1 METBO_RS11680 (R)-citramalate synthase
Query= curated2:Q8TYB1 (499 letters) >NCBI__GCF_000191585.1:WP_013645928.1 Length = 501 Score = 532 bits (1371), Expect = e-156 Identities = 269/490 (54%), Positives = 365/490 (74%), Gaps = 5/490 (1%) Query: 4 RVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIAG 63 + RIFDTTLRDGEQTPGVSLT ++K+ IA KLD GVD IEAG + S GE E +++I Sbjct: 2 KARIFDTTLRDGEQTPGVSLTPDQKLRIAVKLDNLGVDVIEAGSAITSSGEREGIKSIVS 61 Query: 64 EELDAEICGLARCVKGDIDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALERAIEGVE 123 E L AEIC AR ++ D+DAA++ VD VH+ + TSD+H+ +KL +REE AI+ VE Sbjct: 62 EGLSAEICSFARAMRIDVDAALECGVDSVHLVVPTSDLHIEHKLRKTREEVKATAIDAVE 121 Query: 124 YASDHGVTVEFSAEDATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPPEMYRLTAEV 183 YA D+G+ VE SAEDATR+D +YL +V+ +EAGA R+ DTVG++TP + Y + Sbjct: 122 YAVDNGLLVELSAEDATRSDYNYLKQVFNEGIEAGARRICACDTVGMLTPEKAYEFYGGL 181 Query: 184 VDAVDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNASLEQVVMALKAL 243 + VP+S HCHNDFG+AVAN+L+ + GA Q HVTVNGIGERAGNASLE+VV++L +L Sbjct: 182 TQ-LGVPLSAHCHNDFGLAVANTLSGLRGGASQAHVTVNGIGERAGNASLEEVVVSLYSL 240 Query: 244 YDIELDVRTEMLVELSRLVERLTGVVVPPNTPIVGENAFAHESGIHSHGVIKKAETYEPI 303 Y+ + ++ EML E S+ V R+TG+ + PN IVGENAFAHESGIHS GVIKKAETYEPI Sbjct: 241 YNSKTNINIEMLYETSKTVARMTGIYLQPNKAIVGENAFAHESGIHSDGVIKKAETYEPI 300 Query: 304 RPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLDEIVRRVKELGDKGKRVTEDDL 363 PE VGH+RR V+GKH G H I+K+++EMG+ V + + ++I +RVK LGD GK VT+ DL Sbjct: 301 TPELVGHKRRFVMGKHVGSHIIRKRIKEMGLRVDDARFEQIFQRVKALGDMGKCVTDVDL 360 Query: 364 EAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTASVRVYLDGEEHEAASTGVGSVDAAI 423 +AIA D +G + +E V+LEE+ +++GNK TPTASV++ +DG E A GVG VDAAI Sbjct: 361 QAIAEDALGVL--AEKPVELEELTIVSGNKVTPTASVKINVDGSEKVEAGVGVGPVDAAI 418 Query: 424 RALREAIEELGMDVELKEYRLEAITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASV 483 A++++I ++ D++L+EY ++AITGGTDAL +V V+L++ D N+ TAR DI+MASV Sbjct: 419 VAIKKSIMDVA-DIQLEEYHVDAITGGTDALIDVVVKLKNGD-NIVTARSTQPDIIMASV 476 Query: 484 KAFVRGVNRL 493 +A + GVN++ Sbjct: 477 EAVLGGVNKI 486 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: 665 Number of extensions: 29 Number of successful extensions: 7 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: 501 Length adjustment: 34 Effective length of query: 465 Effective length of database: 467 Effective search space: 217155 Effective search space used: 217155 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