Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_053544286.1 CDES_RS03455 acyl-CoA carboxylase subunit beta
Query= SwissProt::P53003 (546 letters) >NCBI__GCF_001277995.1:WP_053544286.1 Length = 543 Score = 665 bits (1716), Expect = 0.0 Identities = 328/534 (61%), Positives = 410/534 (76%), Gaps = 1/534 (0%) Query: 13 AEAPDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERIDMLLDEGSFVELD 72 A PDI+TTAGK+ADL R EA E+AV K HA G+ TARER+D LLDEGSF+E D Sbjct: 11 ANLPDINTTAGKIADLKARRAEAHFPMGEKAVEKVHAAGRLTARERLDYLLDEGSFIETD 70 Query: 73 EHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSLGEVFGEKIVKVM 132 + ARHR+T FG+ + RP DG+VTGWGT+DGR VC+FSQD TVFGG+LGEV+GEK++K+M Sbjct: 71 QLARHRTTAFGLGSKRPATDGIVTGWGTIDGREVCIFSQDGTVFGGALGEVYGEKMIKIM 130 Query: 133 DLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQISLIMGPCAGGAV 192 +LA+ TG PL+G+ + GARIQ+G +L ++ F +N ASGVIPQIS+IMG CAGG Sbjct: 131 ELAIDTGRPLIGLYEGAGARIQDGAVSLDYISQTFYQNIQASGVIPQISVIMGACAGGNA 190 Query: 193 YSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNERSGNAHYLATDED 252 Y PA+TDF VMVD++S MF+TGPDVIKTVTGE+++ E+LGGA TH +GN+HY A ++ Sbjct: 191 YGPALTDFVVMVDKSSKMFVTGPDVIKTVTGEEITQEELGGATTHMVTAGNSHYTAQTDE 250 Query: 253 DAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLELDALVPDSPNQPYDMR 312 +A+ +V++L+SFLPSNN S +P E EEG + D + DL+LD ++PDS PYD+R Sbjct: 251 EALDWVQDLISFLPSNNRSFAPAEDFDE-EEGGIEDNITADDLKLDEIIPDSATVPYDVR 309 Query: 313 EVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGTLDIDASEKAARF 372 +VI L D+GE+LE+ A A N++ FGRIEG SVG VANQP Q AG LDID+SEKAARF Sbjct: 310 DVIQCLTDDGEYLEIQADRAENVVIAFGRIEGQSVGFVANQPTQFAGCLDIDSSEKAARF 369 Query: 373 VRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVPLVTVITRKAYGG 432 VR CDAFNIP++ LVDVPGFLPG GQE+ GI+RRGAKLLYAY EATVP +TV RKAYGG Sbjct: 370 VRTCDAFNIPIVMLVDVPGFLPGAGQEYGGILRRGAKLLYAYGEATVPKITVTMRKAYGG 429 Query: 433 AYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGEDVEALRARLQQE 492 AY VMGSK LG+D+NLAWPTAQIAVMGA GA +YR++L A +G D AL ++E Sbjct: 430 AYCVMGSKGLGSDVNLAWPTAQIAVMGAAGAVGFIYRKELMAADAKGLDTVALAKSFERE 489 Query: 493 YEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKKHGNIPL 546 YED + NPY+AAERG +D+VI PS TRG +AR LR+L K PA+KHGN+PL Sbjct: 490 YEDHMLNPYLAAERGLIDAVILPSETRGQIARNLRLLKHKNVTRPARKHGNMPL 543 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: 802 Number of extensions: 23 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: 543 Length adjustment: 35 Effective length of query: 511 Effective length of database: 508 Effective search space: 259588 Effective search space used: 259588 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