Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate 351389 BT1861 2-isopropylmalate synthase (NCBI ptt file)
Query= BRENDA::Q58787 (491 letters) >FitnessBrowser__Btheta:351389 Length = 498 Score = 348 bits (892), Expect = e-100 Identities = 210/494 (42%), Positives = 294/494 (59%), Gaps = 17/494 (3%) Query: 5 IFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKEGL 64 IFDTTLRDGEQ PG L +K+++AK L+ LGVDVIEAG I+S G+ + I+K Sbjct: 7 IFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIEISKAVT 66 Query: 65 NAEICSFVRALPVDIDAALEC----DVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAV 120 IC+ RA+ DID A++ +H + TS H+KYK +E++E A+ AV Sbjct: 67 WPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIERAVAAV 126 Query: 121 EYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKK 180 +YA+ VE AEDA R+D +L ++ K GA V + DT G P + K Sbjct: 127 KYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEYGAKIKY 186 Query: 181 ITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVA 236 + ++V N +S HCHND GMATANT + VL GA Q VT+NGIGERAGN +LEE+ Sbjct: 187 LIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTALEEIAM 246 Query: 237 ALKILYGYD--TKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIKN 294 +K + D T I +K+Y SR+VS LM +PV PNKAIVG NAFAH +GIH DG++KN Sbjct: 247 IIKSHHEIDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQDGVLKN 306 Query: 295 TETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFGDLG 353 ETYE I P VG + I+L SGR ALK +L L+G+N+ E+L+K+YE + D Sbjct: 307 VETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFLKLADKK 366 Query: 354 KYISDADLLAIVREVTGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIETAYG 413 K I+D D+L + + +IKL+ L V SG + +AS+ L+ GE A G Sbjct: 367 KDINDDDVLVLAG--ADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFE--ACASG 422 Query: 414 VGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVRKSDAD 473 GPVDAAI A++K + + L E+ ++AI G+D + +V +++ +I ++ D Sbjct: 423 NGPVDAAIKALKKIVD--RHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD 480 Query: 474 IIRASVDAVMEGIN 487 II ASV+A ++ IN Sbjct: 481 IIAASVEAYIDCIN 494 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: 658 Number of extensions: 35 Number of successful extensions: 8 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: 498 Length adjustment: 34 Effective length of query: 457 Effective length of database: 464 Effective search space: 212048 Effective search space used: 212048 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