Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_244148019.1 PAES_RS03690 citramalate synthase
Query= BRENDA::Q58595 (518 letters) >NCBI__GCF_000020625.1:WP_244148019.1 Length = 550 Score = 226 bits (576), Expect = 2e-63 Identities = 166/520 (31%), Positives = 277/520 (53%), Gaps = 36/520 (6%) Query: 24 VYIFDTTLRDGEQTPGVSLTPEEKIDIAIKLDDLGVDVIEAGFPVSSLGEQEAIKKICSL 83 + ++DTTLRDG Q ++L+ ++K+ IA KLD+ G D IE G+P S+ ++E +K L Sbjct: 19 IELYDTTLRDGTQGEKINLSVQDKLLIAEKLDEFGADYIEGGWPSSNPKDEEFFRKALGL 78 Query: 84 NL-DAEICGLARAVKKDIDVAIDCGVDR--------IHTFIATSPLHRKYKLKKSKEEII 134 L +A+IC +K ++A D + I F T H L EE Sbjct: 79 RLSNAKICAFGSTARKPDNIANDPNLAGLLASETPVITIFGKTWKAHSAVSLGLCDEENA 138 Query: 135 DIAVDAIEYIKEHGIRVEFSAE---DATRTEIDYLIEVYKKAVDAGADIINVPDTVGVMI 191 ++ ++E++K+ G V F AE D + + I++ A +AGAD + + DT G + Sbjct: 139 ELIYRSVEHLKKEGREVLFDAEHFFDGYKDNPAFAIKMLLSAEEAGADRLVLCDTNGGTL 198 Query: 192 PRAMYYLINELKKEIKVPISVHCHNDFGLAVANSLAAVEAGAEQVHCTINGLGERGGNAA 251 P +Y ++ ++ VP+ +H HND LAVAN+L+A+ AGA V TING+GER GNA Sbjct: 199 PNEIYEIVKDVASSTTVPLGIHSHNDGDLAVANALSALRAGAMHVQGTINGIGERCGNAN 258 Query: 252 LEEVVMSLMSIYGVKTNIKTQKLYEISQL--VSKYT-EIKVQP--NKA-IVGENAFAHES 305 L ++ +++ +K N + + +++QL +SK+ EI P N+A VG +AFAH+ Sbjct: 259 LISIIPNVV----LKMNGRFRHKLQLNQLTPLSKFVYEILNMPPDNRAPFVGRSAFAHKG 314 Query: 306 GIHAHGVLAHALTYEPIPPELVGQKRKIILGKHTGTHAIEAKLKELGIEVGKDINKDQFD 365 GIH V+ + YE I P+ VG ++++++ + +G I K ELGI + D N F Sbjct: 315 GIHVSAVMKESSLYEHIDPKSVGNRQRVLVSELSGQSNIRYKANELGINLPAD-NAALFK 373 Query: 366 EIVKRIKALGDKGKR--VTDRDVEAIVEDVVGKLAKKDRVVELEQIAVMTGNRVIPTASV 423 +V+RIK L +G + V + E ++ +G+ V+E ++ + +G Sbjct: 374 TLVQRIKTLEHEGFQFDVAEASFELLLRHQLGQFKPFFTVLE-SKLHIESGKNRESVDQA 432 Query: 424 ALKIE--EEIKKSSAIGVGPVDAAVKAIQKAIG------EKIKLKEYHINAI--TGGTDA 473 LKIE +EI+ ++A G GPV+A KA++K++ ++L +Y + + GT A Sbjct: 433 VLKIEVCDEIELTAADGDGPVNALDKALRKSLRGFYPEIRSMRLVDYKVRVLEEKKGTSA 492 Query: 474 LAEVIVTLEGYGREITTKAASEDIVRASVEAVIDGINKIL 513 V++ +T S +I+ AS++A+ D IN L Sbjct: 493 KVRVLIESSDGQNSWSTVGVSPNIIDASLQALSDSINYYL 532 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: 567 Number of extensions: 24 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: 550 Length adjustment: 35 Effective length of query: 483 Effective length of database: 515 Effective search space: 248745 Effective search space used: 248745 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