Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_012475116.1 CPHAMN1_RS08580 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000020545.1:WP_012475116.1 Length = 522 Score = 329 bits (843), Expect = 2e-94 Identities = 205/508 (40%), Positives = 291/508 (57%), Gaps = 32/508 (6%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61 +V + DTTLRDGEQ+PG SL +EK+ IA +++ L DIIEAG +S + E +R++ Sbjct: 4 KVLIFDTTLRDGEQSPGASLNLQEKVEIARQLEKLNVDIIEAGFPASSPLQFEAVRRVGE 63 Query: 62 EGLRAEICSFARAVREDI----DAAISCDVDSVHLVVPTSDLHLEHK---------LRKT 108 E + + + RA+ DI +A + +H + TS +H+ K L + Sbjct: 64 ESGKT-VAALCRAMEHDIKSAHEALRNARYPRIHTFISTSAIHIMGKFSNDRYGKTLAEK 122 Query: 109 REEVLEQAVDCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGI 168 ++ +L+ AVD YA VE SAED+ R+D +L I I AGA + DT G Sbjct: 123 QQTILKMAVDAVSYAKTFTDDVEFSAEDAGRTDPAYLAEIIEAVISAGASTVNIPDTTGY 182 Query: 169 LTPERSYEFYRGLSELG--------APLSVHCHNDFGLAVANSLAGLRAGASEVHATING 220 P EF R +++L A +SVHCHND GLAVAN+L+ + GA + +ING Sbjct: 183 TWPS---EFGRKIADLKKRVPNIDHAVISVHCHNDLGLAVANTLSSVENGARQAECSING 239 Query: 221 IGERAGNAALEEVVVALK---SLYDVDTSINIEMLYETSRMVARMTGVYLQPNKAIVGEN 277 IGERAGNA+LEE+V+AL L++ T I E +Y TSRMV+ TG+ +QPNKAIVG+N Sbjct: 240 IGERAGNASLEEIVMALSVRSDLHNFSTGIVTEEIYNTSRMVSSFTGLIVQPNKAIVGDN 299 Query: 278 AFAHESGIHADGVLKKAETYEPITPEMVGHGR-GFVMGKHIGTHALRKRLDELGMKVADD 336 AFAHESGIH DG+LK TYE +TPE VG + V+G+H G H L+ RL LG KV Sbjct: 300 AFAHESGIHQDGMLKNRHTYEVMTPESVGVPQTTIVLGRHSGKHGLQARLSALGYKVTGA 359 Query: 337 KLMEIFRRVKTLGDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPTASVK 396 +L ++ R +L D K + D DL+ + D L + + ++L + I SG PTA+V+ Sbjct: 360 ELETVYARFVSLADKKKEIYDDDLRVLMGDELNKLIEP-LELDYLHINSGTASIPTATVR 418 Query: 397 LRVDDREVLEAGTGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLR 456 +R + E+ TG GPVDA AI+++L L Y V + T G AL + +KL Sbjct: 419 IRSKGKTYEESSTGDGPVDACFKAIERALS--LGSLLHSYSVRSTTAGRQALGEATVKLN 476 Query: 457 HGDRIISARSTQPDIIMASVEAFLSGVN 484 DR+ + R DII AS +A+L ++ Sbjct: 477 CDDRLFTGRGVSTDIIEASAKAYLQALS 504 Lambda K H 0.317 0.135 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: 598 Number of extensions: 24 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: 496 Length of database: 522 Length adjustment: 34 Effective length of query: 462 Effective length of database: 488 Effective search space: 225456 Effective search space used: 225456 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 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