Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CA265_RS16635 CA265_RS16635 methylmalonyl-CoA carboxyltransferase
Query= BRENDA::Q9LDD8 (587 letters) >FitnessBrowser__Pedo557:CA265_RS16635 Length = 513 Score = 256 bits (655), Expect = 1e-72 Identities = 163/505 (32%), Positives = 259/505 (51%), Gaps = 29/505 (5%) Query: 68 MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126 M+ ++ L+ I + GGG+ + + KL RERI L+D GS F E+ + H Sbjct: 1 MDKKIALLKDKINQANLGGGQARIDSQHKKGKLTARERIHFLMDEGS-FEEIGMMVTHRS 59 Query: 127 ----LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182 + E G++TG G + GR+ + D TV GG+ +K + ++A + Sbjct: 60 TDFGMEREKYLGDGVVTGYGTVSGRLTYVFSQDFTVFGGSLSETHAEKICKLMDMAMKNG 119 Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242 P I L DSGGA + E + +FY ++V +S IPQ++ ++G C G Y P Sbjct: 120 APLIGLNDSGGARIQ---EGVVSLGGYADIFY-KNVQASGVIPQLSAIMGPCAGGAVYSP 175 Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302 A+ D +MV+ +F+ GP +VK T EEV++E+LGGA+ H T SGV+ + +E+ + Sbjct: 176 AITDFILMVENTSYMFVTGPNVVKTVTHEEVTSEELGGASTHATKSGVTHFACANEIEAI 235 Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362 N +K L Q E + +L Y+ EL + P + Q +D+R +I+ + Sbjct: 236 ----NHLKKLLSYMPQNCEEI--ADHLPYETADESRPELNTFMPENASQPYDIREVISAV 289 Query: 363 VDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQ 417 D F E Y +V GFAR+ G+++GI+ N G+L + S+ K A F+ C Sbjct: 290 ADTDSFLEVHAAYAENIVVGFARLAGRSIGIVANQPAYLAGVLDSNSSTKAARFVRFCDC 349 Query: 418 RKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMC 477 IPL+ +++ GF+ G+ E NGI GAK++ A S A VP+IT+IT ++G M Sbjct: 350 FNIPLLVFEDVPGFLPGTDQEWNGIITNGAKLLYAFSEATVPRITVITRKAYGGAYDVMN 409 Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537 + D + WP+A I +MG AA ++ + E + ++ KW E+E K D + Sbjct: 410 SKHIGADMNYAWPSAEIAVMGAKGAAEIIFKREITSAEKPEEKWLEKE-----KLYSDIF 464 Query: 538 EREANPYYSTARLWDDGVIDPCDTR 562 ANPY + R + D VI+P TR Sbjct: 465 ---ANPYRAAERGFVDEVIEPAQTR 486 Lambda K H 0.320 0.138 0.408 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: 721 Number of extensions: 33 Number of successful extensions: 6 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: 587 Length of database: 513 Length adjustment: 36 Effective length of query: 551 Effective length of database: 477 Effective search space: 262827 Effective search space used: 262827 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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