Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate 208494 DVU2981 2-isopropylmalate synthase (TIGR)
Query= BRENDA::Q58787 (491 letters) >FitnessBrowser__DvH:208494 Length = 509 Score = 378 bits (971), Expect = e-109 Identities = 218/501 (43%), Positives = 306/501 (61%), Gaps = 18/501 (3%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 +RIFDTTLRDGEQ+PG ++ +KL +A +L LGVD+IEAG S G+ E ++ I K Sbjct: 5 IRIFDTTLRDGEQSPGATMNIKEKLRLAHQLQTLGVDIIEAGFPAASPGDFESVRAIAKT 64 Query: 63 GLNAEICSFVRALPVDIDAALE--CDVDS--VHLVVPTSPIHMKYKLRKTEDEVLETALK 118 + RALP DID A + C +S +H + TSP+HM+YKLRKT DEV+ Sbjct: 65 VKGMTVAGLCRALPADIDRAWDAVCVAESPRLHTFLATSPVHMQYKLRKTPDEVVRMVDA 124 Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178 AV +A H VE SAEDA+RSD +FL+++F + GA + + DTVG P++ L Sbjct: 125 AVRHAAGHTSNVEFSAEDASRSDRDFLVRVFTTAIEAGATTINIPDTVGYAQPEEFGALV 184 Query: 179 KKITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234 + + EN SVHCHND G+ ANT +A+ GA Q VT++GIGERAGNA+LEE+ Sbjct: 185 RYVIENTPNAHKAVFSVHCHNDLGLGVANTLAALRAGARQAEVTISGIGERAGNAALEEL 244 Query: 235 VAALKI---LYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGL 291 V AL+ +G DT I E+LY R++S ++ P+P NKAIVG NAFAHE+GIH DG+ Sbjct: 245 VMALRTRHDYFGLDTGIVTEQLYPTCRLLSMIIGQPIPANKAIVGANAFAHESGIHQDGM 304 Query: 292 IKNTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG 350 +K+ ETYE + PE +G R ++LGKHSGR A+K KL+ +G + ++QLN +++ VK+ Sbjct: 305 LKHRETYEIMTPESIGRTRTELVLGKHSGRNAVKNKLEELGYRLEEDQLNTVFDAVKQLA 364 Query: 351 DLGKYISDADLLAIVREVTGKLVEEKIKLDELTV-VSGNKITPIASVKLHYKGEDITLIE 409 D K I D D+ A+V E + + ++ +L L+V S + P A+V + GE T+ Sbjct: 365 DKKKQIHDEDVEALVLEEVYR-IPDRYRLVNLSVQCSDTGMPPTAAVVMEVDGE--TMRH 421 Query: 410 TAYGVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVRK 469 +G GP+DA NA+ + +L Y V AI GGTDA EV V++R+ R Sbjct: 422 AGFGAGPIDAVFNAIAHIVGRTP--QLERYSVTAITGGTDAQGEVTVRVRENGGTAVGRG 479 Query: 470 SDADIIRASVDAVMEGINMLL 490 S DII AS A + +N L+ Sbjct: 480 SHPDIIIASARAYLNALNRLV 500 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: 622 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: 509 Length adjustment: 34 Effective length of query: 457 Effective length of database: 475 Effective search space: 217075 Effective search space used: 217075 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