Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_084056961.1 B9A12_RS05830 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_900176285.1:WP_084056961.1 Length = 504 Score = 368 bits (945), Expect = e-106 Identities = 208/504 (41%), Positives = 305/504 (60%), Gaps = 18/504 (3%) Query: 13 EVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAR 72 ++ IFDTTLRDGEQ PG L +KL IA +L +GVD IEAGF +S +LKA++ +A Sbjct: 4 KIHIFDTTLRDGEQVPGAKLNRRQKLEIAEQLARLGVDVIEAGFPCSSPEDLKAVQTVAE 63 Query: 73 EELDAEVCSMARMVKGDVDAAVEA----EADAVHIVVPTSEVHVKKKLRMDREEVLERAR 128 + + +AR V+ D+D A EA E +H+ + +S++H++KKLR DRE L +A Sbjct: 64 QVKGPVIAGLARAVQQDIDIAWEAVKKAERPRIHVFLGSSDIHLQKKLRRDRESALHQAV 123 Query: 129 EVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLA 188 E V+YA+ + VE STED +R++ +YL V +AC++AGA + DTVG PE Sbjct: 124 EAVKYAKKYCEDVEYSTEDASRSDFDYLCRVIEACIQAGATVINVPDTVGYALPEQYGEL 183 Query: 189 VKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEE 246 ++ LRE+V + VILSVHCH+D G+A AN++AAVR GA QV T+NG+GERAGNA+LEE Sbjct: 184 IRNLREKVPALDKVILSVHCHNDLGLAVANSLAAVRNGAEQVECTINGVGERAGNASLEE 243 Query: 247 VVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADG 303 +V+ + E + T + T+ + S++V RL + V PNKA+VG NAF H SGIH DG Sbjct: 244 IVMAIRTRESFFDAHTTLNTKEIYRTSRMVSRLMNIPVQPNKAIVGSNAFAHSSGIHQDG 303 Query: 304 ILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRL 362 ILKD STYE I PE VG VL G + +R +L+++G ++ DEQ ++ +R + Sbjct: 304 ILKDRSTYEIIRPEDVGIKAHSLVLTARSGRAALRHRLEELGYELTDEQFQKVHKRFLNV 363 Query: 363 GDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAAS 422 DR K I+ DL I E L + +E + T++G P AS+ + D + A+ Sbjct: 364 ADRKKEISSQDLATIVEIELTKVSE-TYTFDSLQTMSGNTMQPLASVTLIKDDEKITDAA 422 Query: 423 TGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHSG 482 TG GPV+A +ER + + G EL +Y +A+T G DA+ V++ E ++SG Sbjct: 423 TGNGPVNAVFNCIERIVGESG---ELRDYDLKAVTTGKDALGEAMVRV---EIRGAIYSG 476 Query: 483 -SSREDIVVASLEAFIDGINSLMA 505 + D++ AS A+++ N A Sbjct: 477 IGTSPDVIEASARAYVNAFNRFFA 500 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: 603 Number of extensions: 28 Number of successful extensions: 5 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: 504 Length adjustment: 34 Effective length of query: 475 Effective length of database: 470 Effective search space: 223250 Effective search space used: 223250 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 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