Align 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate 207383 DVU1914 2-isopropylmalate synthase/homocitrate synthase family protein
Query= curated2:B8I1T7 (508 letters) >MicrobesOnline__882:207383 Length = 538 Score = 188 bits (477), Expect = 5e-52 Identities = 159/526 (30%), Positives = 254/526 (48%), Gaps = 36/526 (6%) Query: 1 MARTIKIFDTTLRDGEQTPGVNLNLQEKLEIAKQLVRLGVDVIEGGFAIASPGDFESIMT 60 M R I ++DTTLRDG Q+ +NLN +KL+IA +L LG+ IEGG+ ++P D Sbjct: 1 MRRQIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKE 60 Query: 61 LSR-NLKGVTIASLCR----SVEKDIDRAWEAVQYAESPRIHTFIATSDIHMKYKLKMTE 115 + NLK I++ S + D +A+ A + F + + H + L++ Sbjct: 61 IRNYNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDG 120 Query: 116 EEVLERAVSMVKRAKGYCSNVEFSAE---DASRTREEFLYRVVEAVIKAGATTVNIPDTV 172 L+ + K + V F AE D R + V+ +AG + + DT Sbjct: 121 RRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTN 180 Query: 173 GYSTPLEFGRLIRNIRNNVPNIDKADISVHCHNDLGLAVANSLAAVENGAVQVECTINGL 232 G + P E ++ +R +P +A + +H HND +AVANS+AAV+ GAVQV+ T+NG+ Sbjct: 181 GGTLPHEVHDIVTAVREQLP---EAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGV 237 Query: 233 GERAGNAALEEIIMGINTRK-DYYDITHRIDTTQIYRASRLVSSLTGVNVQPNKAIVGAN 291 GER GNA L +I + + Y Q+ S VS +T + + VG + Sbjct: 238 GERCGNANLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRS 297 Query: 292 AFAHESGIHQHGVLSEKTTYEIMTPESVGMGTNRMVLGKLSGRHAFEDRLKEMGYSLSDE 351 AFAH+ G+H V T YE +TPESVG R+++ +L+GR + G+ L + Sbjct: 298 AFAHKGGVHVSAVNRNATLYEHITPESVG-NHQRVLITELAGRSNIVSLARRFGFHLDKD 356 Query: 352 E--VKTAFAKFKDLAD--KKKVVTDKDIEALVDENIA---VPEIFVIDSFQI---NSGNK 401 E VK + K A + +E L+ +A V E F + F++ N Sbjct: 357 EPVVKGLMNELKKKASLGYDYAAAEASVELLLLRKLARRGVREFFKLIQFRVLESKQEND 416 Query: 402 MISTSTVSVRKDEEIITE--AATGDGPVDAAFNAVERATGV------NAELVHYRIKAVT 453 + S SV + E I E AATG GPV+A NA+ +A L+ ++++ +T Sbjct: 417 LEPMSEASVMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLT 476 Query: 454 -----EGKDALGEVTVKISNNNSIFMGKGVSTDIIEASVKAYLNAI 494 G + V ++ + +S ++ GVS +IIEAS +A +++ Sbjct: 477 GTETDGGTASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSM 522 Lambda K H 0.315 0.131 0.357 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: 530 Number of extensions: 23 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: 508 Length of database: 538 Length adjustment: 35 Effective length of query: 473 Effective length of database: 503 Effective search space: 237919 Effective search space used: 237919 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 (21.6 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