Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_078428591.1 BK574_RS10690 citramalate synthase
Query= BRENDA::Q58595 (518 letters) >NCBI__GCF_002019605.1:WP_078428591.1 Length = 542 Score = 244 bits (624), Expect = 4e-69 Identities = 166/522 (31%), Positives = 284/522 (54%), Gaps = 31/522 (5%) Query: 23 RVYIFDTTLRDGEQTPGVSLTPEEKIDIAIKLDDLGVDVIEAGFPVSSLGEQEAIKKICS 82 +V+++DTTLRDG Q GVSL+ E+K+ IA KLD+LG+ IE G+P S+ + K+ Sbjct: 5 KVFLYDTTLRDGTQGEGVSLSVEDKLKIAKKLDELGIHYIEGGWPGSNPKDMNFFGKVKD 64 Query: 83 LNL---------DAEICGLARAVKKDIDVAIDCGVDRIHTFIATSPLHRKYKLKKSKEEI 133 L L G+ +++ ++ GV + F T + L+ + +E Sbjct: 65 LKLKNATVTAFGSTRRMGVTPDKDQNLQRILESGVKSVAIFGKTWDFQVTHALQTTLDEN 124 Query: 134 IDIAVDAIEYIKEHGIRVEFSAE---DATRTEIDYLIEVYKKAVDAGADIINVPDTVGVM 190 + + D+++Y+KE+G+ V F AE D + +Y I+ KKA +AGAD + + DT G Sbjct: 125 LSMIYDSVKYLKENGLEVIFDAEHFFDGYKRNAEYAIKAIKKAEEAGADCVTLCDTNGGS 184 Query: 191 IPRAMYYLINELKKEIKVPISVHCHNDFGLAVANSLAAVEAGAEQVHCTINGLGERGGNA 250 +P + ++ + +E+ + + +HCHND LAVAN+L AV++GA QV TING GER GN Sbjct: 185 LPDEVKSIVQHVVQELSIQVGIHCHNDGELAVANTLVAVQSGATQVQGTINGYGERCGNV 244 Query: 251 ALEEVVMSLMSIYGVKTNIKTQKLYEISQLVSKYT-EIKVQ---PNKAIVGENAFAHESG 306 L ++ +L G + I++Q+L ++ VSKY EI Q N+ VG++AFAH+ G Sbjct: 245 NLISLIPNLQLKMGYEC-IESQELTNLTS-VSKYVHEIANQVPPSNQPFVGKSAFAHKGG 302 Query: 307 IHAHGVLAHALTYEPIPPELVGQKRKIILGKHTGTHAIEAKLKELGIEVGKDINKDQFDE 366 +H VL H TYE I PE +G KR++++ + +G + K KE +++ K N E Sbjct: 303 MHVSAVLKHPETYEHIEPEAIGNKRRVLVSELSGQSNVLFKAKEWNLDLDK--NNPATKE 360 Query: 367 IVKRIKALGDKGKR--VTDRDVEAIVEDVVGKLAKKDRVVELEQIAVMTGNRVIPT-ASV 423 I+++IK L G + + E +V+ +G+ + ++ + + GN+ T A V Sbjct: 361 IIEQIKELELNGYQYEAAEASFELVVKKGLGEHREFFKLDHFKILIENDGNQSFTTEAVV 420 Query: 424 ALKIEEEIKKSSAIGVGPVDAAVKAIQKAIGE------KIKLKEYHINAI--TGGTDALA 475 L + ++ ++A G GPV+A A++KA+ + ++ L +Y + + T T + Sbjct: 421 KLVVNDQEVLTAAEGNGPVNALDHALRKALEQFYPCINQMYLSDYKVRVLDETDATASRV 480 Query: 476 EVIVTLEGYGREITTKAASEDIVRASVEAVIDGINKILAKRE 517 V++ + +T S +I++AS A+ID + L K++ Sbjct: 481 RVLIESSDGKEKWSTIGVSGNIIKASWYALIDSVQYYLLKQD 522 Lambda K H 0.316 0.135 0.368 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: 619 Number of extensions: 26 Number of successful extensions: 4 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: 518 Length of database: 542 Length adjustment: 35 Effective length of query: 483 Effective length of database: 507 Effective search space: 244881 Effective search space used: 244881 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