Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate Dsui_3519 Dsui_3519 2-isopropylmalate synthase, bacterial type
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__PS:Dsui_3519 Length = 513 Score = 383 bits (983), Expect = e-110 Identities = 214/499 (42%), Positives = 313/499 (62%), Gaps = 16/499 (3%) Query: 16 IFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAREEL 75 IFDTTLRDGEQ+PG ++T EEKLR+AR+L+ + VD IEAGFAAAS G+ AI IA Sbjct: 7 IFDTTLRDGEQSPGASMTKEEKLRVARQLERMRVDVIEAGFAAASPGDFDAIHAIAEAIK 66 Query: 76 DAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERAREVV 131 D+ VCS+AR + D+ A EA A +H + TS +H++KKLRM ++V+E+A + + Sbjct: 67 DSTVCSLARANENDIRRAGEAIKPAARGRIHTFIATSPIHMEKKLRMSPDQVVEQAVKAI 126 Query: 132 EYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKK 191 +AR++ VE S ED R+E+++L +F+A ++AGA + DTVG P +++ Sbjct: 127 GWAREYTNDVEFSAEDAGRSEIDFLCRIFEAVIKAGATTINVPDTVGYNLPSQFAETIRQ 186 Query: 192 LRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVV 249 L ERV + V+ SVHCH+D G+A AN++AAV AGARQV T+NG+GERAGNA+LEEVV+ Sbjct: 187 LIERVPGADKVVWSVHCHNDLGLAVANSLAAVLAGARQVECTINGLGERAGNASLEEVVM 246 Query: 250 VLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILK 306 +++ V+T + T ++ SKLV ++TG V PNKA+VG NAF HESGIH DG+LK Sbjct: 247 ATRTRADIFPVETRVDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAHESGIHQDGVLK 306 Query: 307 DESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLE-ILRRLKRLGD 364 TYE + E VG + + VLGKH G + + +L ++G+D+ E+ L R K L D Sbjct: 307 HRETYEIMRAEDVGWSQNKLVLGKHSGRNAFKTRLAELGIDLPSEEALNAAFARFKELAD 366 Query: 365 RGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAASTG 424 + I + DL+A+ D P + ++ + IP +++ + + G +AAS+G Sbjct: 367 KKHEIFDEDLQALVSDETVTPEQEHYKLVYSQVCSETGEIPESAVTLAVGGAEHKAASSG 426 Query: 425 VGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHSGSS 484 GPVDAT KA+E+ E + Y A+T GTDA V V+L + G IV+ + Sbjct: 427 SGPVDATFKAIEKIAASGA---EQLLYSVNAITTGTDAQGEVTVRL--AKGGRIVNGQGA 481 Query: 485 REDIVVASLEAFIDGINSL 503 DIV+AS +A+++ +N L Sbjct: 482 DTDIVIASAKAYLNALNKL 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: 638 Number of extensions: 32 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: 509 Length of database: 513 Length adjustment: 35 Effective length of query: 474 Effective length of database: 478 Effective search space: 226572 Effective search space used: 226572 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