Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_011778931.1 MVAN_RS08455 acyl-CoA carboxylase subunit beta
Query= SwissProt::P53003 (546 letters) >NCBI__GCF_000015305.1:WP_011778931.1 Length = 542 Score = 745 bits (1923), Expect = 0.0 Identities = 377/546 (69%), Positives = 436/546 (79%), Gaps = 4/546 (0%) Query: 1 MSSATEPVGVPPAEAPDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERID 60 M+S TEP DIHTTAGKLADL +R EA H E AV K HAKGK TARERI Sbjct: 1 MTSVTEPSA---EHEIDIHTTAGKLADLRKRAAEAQHPVGETAVEKVHAKGKLTARERIL 57 Query: 61 MLLDEGSFVELDEHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSL 120 LLDEGSFVELD A+HRS NFG++ +RP GDGVVTG+GT+DGR VCVFSQD TVFGGSL Sbjct: 58 ALLDEGSFVELDALAKHRSKNFGLEHNRPTGDGVVTGYGTIDGRDVCVFSQDATVFGGSL 117 Query: 121 GEVFGEKIVKVMDLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQI 180 GEV+GEKIVKV +LA+KTG PL+GIND GARIQEGV +LGLY+ IF N ASGVIPQI Sbjct: 118 GEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFHNNIKASGVIPQI 177 Query: 181 SLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNER 240 SLIMG AGG VYSPA+TDF +MVDQTS MFITGPDVIKTVTGEDV+ E+LGGA TH + Sbjct: 178 SLIMGAAAGGHVYSPALTDFVIMVDQTSQMFITGPDVIKTVTGEDVTMEELGGAHTHMAK 237 Query: 241 SGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLELDAL 300 SG HY+A+ E DA+ YV++LLS+LP NN + P +P + + + + D DLELD L Sbjct: 238 SGTVHYVASGEQDALDYVRDLLSYLPPNNYAEPPRYPAPHAD-APIEESLTDEDLELDTL 296 Query: 301 VPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGT 360 +PDSPNQPYDM EVITR++D+ EFLEV A +A N++ GFGR++G VG+VANQP Q AG Sbjct: 297 IPDSPNQPYDMHEVITRILDDDEFLEVQAGYAGNIVIGFGRVDGRPVGIVANQPTQFAGC 356 Query: 361 LDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVP 420 LDI+ASEKAARF+R CD FNIP++ LVDVPGFLPGT QE+NGIIRRGAKLLYAY EATV Sbjct: 357 LDINASEKAARFIRTCDCFNIPIVLLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVA 416 Query: 421 LVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGE 480 VTVITRK+YGGAY VMGSK +GAD+ +AWPTAQIAVMGA GA +YR+QL EAA GE Sbjct: 417 KVTVITRKSYGGAYCVMGSKDMGADVVVAWPTAQIAVMGASGAVGFVYRQQLREAAANGE 476 Query: 481 DVEALRARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKK 540 DV+ALR +LQQEYEDTL NPY+AAERGYVD+VI PSHTRG+VA AL++L K P KK Sbjct: 477 DVDALRLKLQQEYEDTLVNPYIAAERGYVDAVILPSHTRGYVATALKLLERKVVQTPPKK 536 Query: 541 HGNIPL 546 HGNIPL Sbjct: 537 HGNIPL 542 Lambda K H 0.318 0.136 0.398 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: 862 Number of extensions: 32 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: 546 Length of database: 542 Length adjustment: 35 Effective length of query: 511 Effective length of database: 507 Effective search space: 259077 Effective search space used: 259077 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: 52 (24.6 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