Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate 8501055 DvMF_1791 2-isopropylmalate synthase (RefSeq)
Query= BRENDA::Q58787 (491 letters) >FitnessBrowser__Miya:8501055 Length = 514 Score = 375 bits (963), Expect = e-108 Identities = 218/500 (43%), Positives = 308/500 (61%), Gaps = 18/500 (3%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 +RIFDTTLRDGEQ+PG ++ +K+ +A++L+ LGVD++EAG +S+G+ E ++ I + Sbjct: 8 IRIFDTTLRDGEQSPGATMNLQEKIRLARQLETLGVDIMEAGFPASSQGDFEAVQAIARA 67 Query: 63 GLNAEICSFVRALPVDIDAALE----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALK 118 E+ RA+P DID A E + +H + TSP+HM+YKLRK D+V+E A+ Sbjct: 68 VKGVEVAGLCRAMPADIDRAWEAVKVAENPRIHTFLATSPVHMQYKLRKEPDQVVEMAVA 127 Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178 AV +A ++ VE SAEDA+RS+ +FL+++F GA + V DTVG P++ L Sbjct: 128 AVRHAAKYTSNVEFSAEDASRSNPDFLVRVFEAVINAGATTINVPDTVGYAQPEEFGRLI 187 Query: 179 KKITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234 + + EN SVHCHND GM ANT +A+ GA Q VT++GIGERAGNASLEE+ Sbjct: 188 RYVIENTPNSHKAVFSVHCHNDLGMGVANTLAALKAGARQAEVTISGIGERAGNASLEEI 247 Query: 235 VAAL---KILYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGL 291 V AL + Y D + E+L+ R++S ++ P+PPNKAIVG NAFAHE+GIH DG+ Sbjct: 248 VMALHTRRDFYQLDCGVVTEQLFPTCRLLSMIIGQPIPPNKAIVGANAFAHESGIHQDGM 307 Query: 292 IKNTETYEPIKPEMVGNRRR-IILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG 350 +KN ETYE + PE +G + +++GKHSGR A+K KLD +G + + QL ++E VK+ Sbjct: 308 LKNRETYEIMTPESIGKTKTDLVIGKHSGRNAVKNKLDELGYRLEEAQLVTVFEAVKKLA 367 Query: 351 DLGKYISDADLLAIVREVTGKLVEEKIKLDELTV-VSGNKITPIASVKLHYKGEDITLIE 409 D K I D D+ A+V E +L + +L L+V S + P A+V + GE Sbjct: 368 DKKKQIYDEDIEALVLEEVYRL-PDLYRLVNLSVQCSDTGMPPTAAVVMDVMGE--VKRA 424 Query: 410 TAYGVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVRK 469 +GVGP+DA N + + I G A + L Y V AI GGTDA EV V+LR+ R Sbjct: 425 AGFGVGPIDAVFNVIGE-IVGRAPV-LERYSVTAITGGTDAQGEVTVRLRQNGSSAVGRG 482 Query: 470 SDADIIRASVDAVMEGINML 489 SD DII AS A + +N L Sbjct: 483 SDPDIILASARAYVNALNRL 502 Lambda K H 0.316 0.136 0.373 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: 601 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: 491 Length of database: 514 Length adjustment: 34 Effective length of query: 457 Effective length of database: 480 Effective search space: 219360 Effective search space used: 219360 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