Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_034275130.1 AMYHA_RS25160 acyl-CoA carboxylase subunit beta
Query= SwissProt::P53003 (546 letters) >NCBI__GCF_000504245.1:WP_034275130.1 Length = 549 Score = 875 bits (2261), Expect = 0.0 Identities = 437/549 (79%), Positives = 475/549 (86%), Gaps = 3/549 (0%) Query: 1 MSSATEPVGVPPAEAP---DIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARE 57 MSSATEP+G A DIHTTAGKLADLYRRN EAVHAGS RAV KQHAKGK+TARE Sbjct: 1 MSSATEPLGGQHGSAEESIDIHTTAGKLADLYRRNDEAVHAGSARAVEKQHAKGKKTARE 60 Query: 58 RIDMLLDEGSFVELDEHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFG 117 RIDMLLD GSFVELDE ARHRSTNFG DA+RPYGDGVVTG+GT+DGR VCVFSQD T+FG Sbjct: 61 RIDMLLDPGSFVELDELARHRSTNFGQDANRPYGDGVVTGYGTIDGRPVCVFSQDVTIFG 120 Query: 118 GSLGEVFGEKIVKVMDLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVI 177 GSLGEV+GEKIVKVMDLA+KTG P++GIN+ GGARIQEGV +LGLY EIF RN ASGV+ Sbjct: 121 GSLGEVYGEKIVKVMDLAIKTGRPIIGINEGGGARIQEGVVSLGLYGEIFTRNVKASGVV 180 Query: 178 PQISLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTH 237 PQISLIMG AGG VYSPA+TDF VMVDQTSHMFITGPDVIKTVTGE+V+FE+LGG R+H Sbjct: 181 PQISLIMGANAGGHVYSPALTDFVVMVDQTSHMFITGPDVIKTVTGEEVTFEELGGGRSH 240 Query: 238 NERSGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLEL 297 N +SGNAHYL DE+DAISYVKELLSFLP NNL+ PVF SVAD + D D EL Sbjct: 241 NTKSGNAHYLGADEEDAISYVKELLSFLPPNNLAEPPVFEAPPHTGNSVADDITDDDREL 300 Query: 298 DALVPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQL 357 D L+PDSPN PYDM EVIT +VD+GEFLEV LFAPN+L GFGR++G SVG+VANQP Q Sbjct: 301 DTLIPDSPNVPYDMHEVITHVVDDGEFLEVHELFAPNVLVGFGRVDGQSVGIVANQPTQF 360 Query: 358 AGTLDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEA 417 AG LDIDASEKAARFVR CDAFN+PVLT VDVPGFLPGT QEWNGIIRRGAKL+YAYAEA Sbjct: 361 AGCLDIDASEKAARFVRTCDAFNVPVLTFVDVPGFLPGTDQEWNGIIRRGAKLIYAYAEA 420 Query: 418 TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAE 477 TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANI+YR+ LA A Sbjct: 421 TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANIVYRKTLANAEA 480 Query: 478 RGEDVEALRARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALP 537 G+D+E LR L QEYEDTLCNPYVAAERGYVDSVIPPSHTRG+VAR+LR+L DKRE P Sbjct: 481 EGQDIEKLRGELIQEYEDTLCNPYVAAERGYVDSVIPPSHTRGYVARSLRILGDKRENQP 540 Query: 538 AKKHGNIPL 546 KKHGNIPL Sbjct: 541 PKKHGNIPL 549 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: 1014 Number of extensions: 39 Number of successful extensions: 3 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: 549 Length adjustment: 36 Effective length of query: 510 Effective length of database: 513 Effective search space: 261630 Effective search space used: 261630 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: 53 (25.0 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