Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_084200258.1 C0029_RS03860 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::SB2B:6937189 (673 letters) >NCBI__GCF_002869505.1:WP_084200258.1 Length = 658 Score = 571 bits (1471), Expect = e-167 Identities = 315/666 (47%), Positives = 437/666 (65%), Gaps = 28/666 (4%) Query: 4 KLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSYLRG 63 KLLIANRGEIA RVIRTARDMG +TVAVYS+AD +A HV+ AD++ +G +A SYL Sbjct: 6 KLLIANRGEIAVRVIRTARDMGYRTVAVYSEADANALHVSEADQAVCIGPAAVNESYLVA 65 Query: 64 ELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAKLIM 123 + I+ A+ GA+AIHPGYGFLSENA F+RACE +GI F+GP DAI+ MGSK +K+ M Sbjct: 66 DNILKAARLTGADAIHPGYGFLSENADFSRACEDAGIVFIGPRPDAIELMGSKRLSKIAM 125 Query: 124 EKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAAIDS 183 +AGVP +PGY DQSD TLLA+A IG+PL++KA+ GGGG+GMR+V EL I + Sbjct: 126 IEAGVPCIPGYQDADQSDDTLLAKAADIGFPLMVKASAGGGGRGMRLVFEARELAEQIRT 185 Query: 184 ARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVEEAP 243 AR EA S+FG+ +L++ER + +PRHVE+QVFAD GN VYL +RDCSIQRRHQKVVEEAP Sbjct: 186 ARSEAESAFGSGELILERAVLEPRHVEIQVFADEHGNAVYLGERDCSIQRRHQKVVEEAP 245 Query: 244 APGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVTEMV 303 +P + LR++MGEAAV AAKA +YRGAGTVEFL+D D +F+F+EMNTRLQVEHPVTE++ Sbjct: 246 SPFVDPQLRQRMGEAAVNAAKACNYRGAGTVEFLVDKDKNFYFLEMNTRLQVEHPVTELI 305 Query: 304 TGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLREPEP 363 TGQDLV WQL VA+G QLPL Q E+ + GHA EVR+YAEDP N F+P +G + PE Sbjct: 306 TGQDLVAWQLKVASGEQLPLTQDEVSLSGHAVEVRLYAEDPRNNFMPQTGTVRLWEYPER 365 Query: 364 SRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNIEFL 423 + +R+D G+++ +S +YDPMIAK+I + R A+ RL A+ D ++ G+ +N FL Sbjct: 366 A-GLRMDHGIQQGQEVSPFYDPMIAKVIAYGSDRAEAIRRLASAVQDTQLLGMNNNKLFL 424 Query: 424 SNIAEHPAFAQANFSTDFIGRY--GDALIGDSRDEADTAFVLAVLTQLRLREA-VSQDVA 480 N+ H FAQ +T FI ++ D + + T A+L Q + A D + Sbjct: 425 QNVLRHEVFAQGEATTAFIEQHFSADISMDQKKPRQATLARAALLFQAQATAAGPGSDAS 484 Query: 481 GHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTESNGRYQLCLNDKLIELS-GS 539 H+P + ++ + L Q+++ +TE NG Y++ + ++ L+ + Sbjct: 485 WHNPAAAATTYQ--------------LAFDGQAQAIAITEGNGSYEVAVGEERHSLTLVA 530 Query: 540 IEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYHFREVLGQVLEETASS-----EDKL 594 + DSE C + ++ ++ G T++L G+ HF ++ V + A++ +L Sbjct: 531 LSDSE--CVYIDNGVRESMRFAFAGNTLYLDDGTGHF--IIENVTYQPAAAAGGAGSGQL 586 Query: 595 KAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGELVSDGT 654 KA M+G +V LV GD V AGQ L+V+EAMKME+ ++A G+V+ G+ V Sbjct: 587 KASMDGAIVDVLVTEGDTVEAGQTLVVLEAMKMEHALKAGISGIVTAISCETGQQVKSKQ 646 Query: 655 LLLALE 660 LL +E Sbjct: 647 LLATIE 652 Lambda K H 0.317 0.134 0.380 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: 1110 Number of extensions: 44 Number of successful extensions: 4 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: 673 Length of database: 658 Length adjustment: 38 Effective length of query: 635 Effective length of database: 620 Effective search space: 393700 Effective search space used: 393700 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 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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