Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF583 PS417_02965 acetyl-CoA carboxylase
Query= BRENDA::Q42523 (734 letters) >FitnessBrowser__WCS417:GFF583 Length = 453 Score = 409 bits (1052), Expect = e-118 Identities = 213/452 (47%), Positives = 293/452 (64%), Gaps = 6/452 (1%) Query: 31 MKPKEQCIEKILVANRGEIACRIMRTAKRLGIQTVAVYSDADRDSLHVKSADEAVRIGPP 90 +KP ++ ++K+L+ANRGEIA RI+R K GI+TVAVYS AD + +HVK ADE++ IGPP Sbjct: 2 LKPAKK-LQKVLIANRGEIALRILRACKEEGIKTVAVYSTADTELMHVKLADESICIGPP 60 Query: 91 SARLSYLSGVTIMEAAARTGAQAIHPGYGFLSESSDFAQLCEDSGLTFIGPPASAIRDMG 150 A SYL I+ AA TGA IHPGYGFL+E++DFA+ E SG FIGP A IR MG Sbjct: 61 LATNSYLKVSNIIAAAEVTGADGIHPGYGFLAENADFAEQVEKSGFAFIGPKAETIRLMG 120 Query: 151 DKSASKRIMGAAGVPLVPGYHGH-EQDIDHMKSEAEKIGYPIIIKPTHGGGGKGMRIVQS 209 DK ++K M AAGVP VPG G +D + ++GYP+IIK GGGG+GMR+V Sbjct: 121 DKVSAKDAMIAAGVPTVPGSDGPLPEDEETALRIGREVGYPVIIKAAGGGGGRGMRVVHK 180 Query: 210 GKDFADSFLGAQREAAASFGVNTILLEKYITRPRHIEVQIFGDKHGNVLHLYERDCSVQR 269 +D ++ + EA A FG + LEKY+T PRH+EVQ+ D G+ +HL +RDCS+QR Sbjct: 181 EEDLIEAAKQTRSEAGAWFGNPMVYLEKYLTNPRHVEVQVLSDGQGHAIHLGDRDCSLQR 240 Query: 270 RHQKIIEEAPAPNISEKFRANLGQAAVSAARAVGYYNAGTVEFIVDTESDQFYFMEMNTR 329 RHQK++EEAPAP + EK R + V A + Y AGT EF+ E+ +FYF+EMNTR Sbjct: 241 RHQKVLEEAPAPGLDEKARQEVLARCVKACIDINYRGAGTFEFLY--ENGRFYFIEMNTR 298 Query: 330 LQVEHPVTEMIVGQDLVEWQIRVANGEPLPLSQSEVPMSGHAFEARIYAENVPKGFLPAT 389 +QVEHPV+EM+ G D+V+ + +A G PL +Q +V M GH+ E RI AE+ PK F+P+ Sbjct: 299 VQVEHPVSEMVTGIDIVKEMLSIAAGNPLSFTQDDVKMHGHSLECRINAED-PKTFIPSP 357 Query: 390 GVLNHYRPVAVSPSVRVETGVEQGDTVSMHYDPMIAKLVVWGGNRGEALVKLKDCLSNFQ 449 G++ H+ VRV++ + G V +YD +I KL+ WG R EA+ ++++ L Sbjct: 358 GLVKHFHAPG-GNGVRVDSHLYSGYKVPSNYDSLIGKLITWGATRDEAMARMRNALDEIV 416 Query: 450 VAGVPTNINFLQKLASHKEFAVGNVETHFIEH 481 V G+ TNI + L + F G V H++EH Sbjct: 417 VDGIKTNIPLHRDLVRDEGFCEGGVNIHYLEH 448 Lambda K H 0.316 0.132 0.386 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: 889 Number of extensions: 42 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: 734 Length of database: 453 Length adjustment: 36 Effective length of query: 698 Effective length of database: 417 Effective search space: 291066 Effective search space used: 291066 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: 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