Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_053544285.1 CDES_RS03450 acyl-CoA carboxylase subunit beta
Query= SwissProt::P53003 (546 letters) >NCBI__GCF_001277995.1:WP_053544285.1 Length = 537 Score = 660 bits (1703), Expect = 0.0 Identities = 322/531 (60%), Positives = 414/531 (77%), Gaps = 1/531 (0%) Query: 16 PDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERIDMLLDEGSFVELDEHA 75 PD+ TTAGKL+DL R EA + +V K H G++TARERI+ LLD+G+FVE+D A Sbjct: 8 PDLTTTAGKLSDLRSRLAEAQAPMGQESVEKAHEAGQKTARERIEYLLDQGTFVEIDALA 67 Query: 76 RHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSLGEVFGEKIVKVMDLA 135 RHRS NFG+DA RP DGVVTG+GT+DGR+VC+FSQD VF G+LGEV GEKIVKVMDLA Sbjct: 68 RHRSKNFGLDAKRPATDGVVTGYGTIDGRKVCIFSQDGAVFDGTLGEVNGEKIVKVMDLA 127 Query: 136 MKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQISLIMGPCAGGAVYSP 195 +KTG PL+ IN+ GARI+EG+ +LG+Y+++F RNT ASG++PQISL+MG AGG VYSP Sbjct: 128 IKTGVPLIAINEGAGARIKEGIVSLGMYSKMFYRNTQASGLVPQISLVMGESAGGNVYSP 187 Query: 196 AITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNERSGNAHYLATDEDDAI 255 A++DF VMV+ TS M++T P++IKTVTG+DV+ E+LGGA TH SG +HY A +E DA+ Sbjct: 188 ALSDFLVMVNGTSQMYVTSPEIIKTVTGDDVTTEELGGATTHMATSGTSHYSAANETDAL 247 Query: 256 SYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLELDALVPDSPNQPYDMREVI 315 +V+ELLS+LPSNN + +P P E+ GS+ + V D D ELD+++PDS +QPYDMR ++ Sbjct: 248 DWVRELLSYLPSNNRAEAPRTP-VEITTGSIQENVTDLDRELDSIIPDSNHQPYDMRTIL 306 Query: 316 TRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGTLDIDASEKAARFVRF 375 +R+VDE EF E+ +A N+LCGF RIEG SVG+VANQP QLAG LDI A EKAARF+R Sbjct: 307 SRVVDEAEFFEIQKDYAENILCGFARIEGRSVGIVANQPTQLAGCLDIKAMEKAARFIRT 366 Query: 376 CDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVPLVTVITRKAYGGAYD 435 CDAFNIP++ VDVPGFLPGT QE+NG+IRRGAKL+YAYAEATV +T+ITRK+ G AY Sbjct: 367 CDAFNIPIVEFVDVPGFLPGTAQEFNGLIRRGAKLVYAYAEATVGKITIITRKSIGTAYS 426 Query: 436 VMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGEDVEALRARLQQEYED 495 +MGSK +GAD+ AWPTA+IAV+ A GA + +Y ++L +AA G+DV + + +YE+ Sbjct: 427 IMGSKDMGADLVYAWPTAEIAVLAASGAVSDIYAKELKQAATEGKDVTEVMKGYEAQYEE 486 Query: 496 TLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKKHGNIPL 546 + NPY+AAERG VD+VIPPS TRG + LR+L K +PAKKHGNIPL Sbjct: 487 SHLNPYLAAERGLVDAVIPPSETRGQILEGLRLLDRKVVNVPAKKHGNIPL 537 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: 739 Number of extensions: 20 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: 546 Length of database: 537 Length adjustment: 35 Effective length of query: 511 Effective length of database: 502 Effective search space: 256522 Effective search space used: 256522 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