Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate Ac3H11_530 2-isopropylmalate synthase (EC 2.3.3.13)
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_530 Length = 512 Score = 360 bits (925), Expect = e-104 Identities = 210/512 (41%), Positives = 315/512 (61%), Gaps = 27/512 (5%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D++ IFDTTLRDGEQ+PG ++T +EKLRIAR+L+ + VD IEAGFAA+S G+ +A++ IA Sbjct: 3 DKLIIFDTTLRDGEQSPGASMTKDEKLRIARQLERLKVDVIEAGFAASSNGDFEAVQAIA 62 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 D+ +CS++R D+ A EA A +H + TS +H++KKLRM E+VLE+A Sbjct: 63 NAIKDSTICSLSRANDRDISRAAEALRGANSARIHTFIATSALHMEKKLRMTPEQVLEQA 122 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 ++ V +AR+ +E S EDG R++ ++L V +A + GA + DTVG PE Sbjct: 123 KQSVRFARNLVADIEFSPEDGYRSDPDFLCRVLEAVITEGATTINVPDTVGYAVPELYGN 182 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVR-AGARQVHVTVNGIGERAGNAAL 244 +K LRER+ + I SVHCH+D GMA AN++A V+ GARQV T+NG+GERAGN +L Sbjct: 183 FIKTLRERIPNSDKAIWSVHCHNDLGMAVANSLAGVKIGGARQVECTINGLGERAGNCSL 242 Query: 245 EEVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHA 301 EE+V+ + ++ +G+D I T+ + S++V + TG V PNKAVVG NAF H SGIH Sbjct: 243 EEIVMAVKTRKDYFGLDLAIDTQHIVAASRMVSQTTGFVVQPNKAVVGANAFAHASGIHQ 302 Query: 302 DGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEI-LRRL 359 DG+LK TYE + E VG + VLGK G + +++L+++GV +D E + + + Sbjct: 303 DGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGVQLDSETEINVAFAKF 362 Query: 360 KRLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTV-----TGKRTIPTASIVVKID 414 K L DR I + D+ A+ D + E F ++ TG++ P A IV +D Sbjct: 363 KELADRKSEIFDEDILALVSD---ESVTAEKEQYGFVSLFQQSETGEQ--PRARIVFTVD 417 Query: 415 GTRKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPE 474 G S G GPVDA++KA+E +K E+V Y A++G T++ V V+L++ Sbjct: 418 GQEVRGESDGNGPVDASLKAIESHVKSGA---EMVLYSVNAISGSTESQGEVTVRLQN-- 472 Query: 475 TGDIVHSGSSREDIVVASLEAFIDGINSLMAR 506 +G +V+ + DIVVAS +A++ +N L ++ Sbjct: 473 SGRVVNGVGADPDIVVASAKAYLSALNKLQSK 504 Lambda K H 0.315 0.134 0.367 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: 585 Number of extensions: 23 Number of successful extensions: 9 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: 509 Length of database: 512 Length adjustment: 35 Effective length of query: 474 Effective length of database: 477 Effective search space: 226098 Effective search space used: 226098 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