Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 3607303 Dshi_0718 carboxyl transferase (RefSeq)
Query= BRENDA::Q9I297 (535 letters) >FitnessBrowser__Dino:3607303 Length = 510 Score = 253 bits (646), Expect = 1e-71 Identities = 177/502 (35%), Positives = 254/502 (50%), Gaps = 42/502 (8%) Query: 39 GGGSAAQARHSARGKLLVRERINRLLDPGSPFLELSALAAHE-----VYGEEVAAAGIVA 93 GGG A A+GKL RERI LLD GS F E H + ++ A G+V Sbjct: 18 GGGEKRIASQHAKGKLTARERIELLLDEGS-FEEFDMFITHRCTDFGMQEQKPAGDGVVT 76 Query: 94 GIGRVEGVECMIVGNDATVKGGTYYPLTVKKHLRAQAIALENRLPCIYLVDSGGANLPRQ 153 G G V G + + D TV GG+ KK + +A+EN P I + DSGGA + Sbjct: 77 GWGTVNGRQVYVFSQDFTVLGGSVSATHAKKICKIMDMAIENGAPVIGINDSGGARI--- 133 Query: 154 DEVFPDREHFGRIFFNQANMSARGI-PQIAVVMGSCTAGGAYVPAMSDETVMVREQATIF 212 E +G +F Q N+ A G+ PQI+++MG C G Y PAM+D MV++ + +F Sbjct: 134 QEGVDSLAGYGDVF--QRNIEASGVVPQISMIMGPCAGGAVYSPAMTDFIFMVKDSSYMF 191 Query: 213 LAGPPLVKAATGEVVSAEELGGADVHCKVSGVADHYAEDDDHALAIARRCV--ANLNWRK 270 + GP +VK T EVV+AEELGGA H + S VAD E+D ALA RR + LN R+ Sbjct: 192 VTGPDVVKTVTNEVVTAEELGGASTHTRKSSVADAAFENDVEALAEVRRLIDFLPLNNRE 251 Query: 271 QGQLQCRAPRAPLY--PA---EELYGVIPADSKQPYDVREVIARLVDGSEFDEFKALFGT 325 +AP P + PA E L +IP + QPYD++E+I ++ D +F E + F Sbjct: 252 ------KAPVRPFFDDPARVEESLDTLIPDNPNQPYDMKELITKVADEGDFYEIQKDFAG 305 Query: 326 TLVCGFAHLHGYPIAILANN-----GILFAEAAQKGAHFIELACQRGIPLLFLQNITGFM 380 ++ GF L G + ++AN G+L ++A+K A F+ IP+L L ++ GF+ Sbjct: 306 NIITGFIRLEGQTVGVVANQPMVLAGVLDIDSARKAARFVRFCDCFEIPILTLVDVPGFL 365 Query: 381 VGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGSFGAGNYGMCGRAYDPRFLWMWPNA 440 G E G+ KHGAKL+ A A VPK TV+ ++G M + + WP A Sbjct: 366 PGTGQEYNGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYVVMSSKHLRGDINYAWPTA 425 Query: 441 RIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAKIKAPILEQYEHQGHPYYSSARLWD 500 + VMG + A ++ + LG E KI A E + +P+ ++ R + Sbjct: 426 EVAVMGAKGATEIIHRA----------DLGDPE--KIAARTAEYEDRFANPFVAAERGFI 473 Query: 501 DGVIDPAQTREVLALALSAALN 522 D VI P TR +A A +A N Sbjct: 474 DEVIMPQSTRRRVARAFAALRN 495 Lambda K H 0.321 0.137 0.409 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: 597 Number of extensions: 22 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: 535 Length of database: 510 Length adjustment: 35 Effective length of query: 500 Effective length of database: 475 Effective search space: 237500 Effective search space used: 237500 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 (21.9 bits) S2: 52 (24.6 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