Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate RR42_RS18165 RR42_RS18165 carbamoyl-phosphate synthase large subunit
Query= SwissProt::P53003 (546 letters) >FitnessBrowser__Cup4G11:RR42_RS18165 Length = 1112 Score = 203 bits (516), Expect = 3e-56 Identities = 162/551 (29%), Positives = 246/551 (44%), Gaps = 42/551 (7%) Query: 9 GVPPAEAPDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERIDMLLDEGSF 68 G A D L D R+ A +AV K HA+G RTARE I L D GSF Sbjct: 579 GAQAGAAVDPAHIRADLRDALARHALTQDAARPQAVDKHHARGGRTARENIAQLCDAGSF 638 Query: 69 VELDEHA----RHRSTNFGMDADRPYGDGVVTGWGTVDGRRV-------CVFSQDFTVFG 117 +E A R R + ++ P DG+VTG GTV+ R V + D+TV Sbjct: 639 IEYGALAIAAQRQRRSVEDLERATP-ADGIVTGIGTVNAERFPATDARCMVLAYDYTVLA 697 Query: 118 GSLGEVFGEKIVKVMDLAMKTGCPLVGINDSGGARI--QEGVAALGLYAEIFKRNTHASG 175 G+ G +K+ +++ LA + P+V + GG R + GL F + SG Sbjct: 698 GTQGFYGHKKLDRMLALARQWRLPVVLFAEGGGGRPGDTDTPVVAGLDCTSFIQFARLSG 757 Query: 176 VIPQISLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGAR 235 +P + ++ G C G D ++ + + + + GP +I+ + E++G Sbjct: 758 QVPLVGIVSGRCFAGNAALLGCAD-VIIATRNATIGMGGPAMIEGGGLGVFAAEEVGPVS 816 Query: 236 THNERSGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADL 295 +G L DE A+ + LS+ +G + D Sbjct: 817 VQAP-NGVIDVLVDDEIAAVETARRYLSYF-----------------QGDLPDWEAGDAR 858 Query: 296 ELDALVPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPM 355 L L+P++ + YDMR V+ L D LE+ A F ++ RIEG + G +AN P Sbjct: 859 ALRHLIPENRLRSYDMRGVLAALADHDSVLELRAAFGAGIITALIRIEGRAFGCIANNPR 918 Query: 356 QLAGTLDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYA 415 L G +D DA++KAARF++ CDA +P+++L D PGF+ G E +R ++L Sbjct: 919 HLGGAIDADAADKAARFMQLCDAHGLPIVSLCDTPGFMVGPEAEKTATVRHVSRLFVTAG 978 Query: 416 EATVPLVTVITRKAYG-GAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAE 474 VP TV+ RK YG GA + G AWP+ + MG +G+ + +R++L E Sbjct: 979 ALRVPFFTVVLRKGYGLGAQAMAGGSFSAPFFTAAWPSGEFGAMGIEGSIRLGFRKEL-E 1037 Query: 475 AAERGEDVEALRARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKRE 534 A ++ EAL AR+ E A +D+VI P+ TR + R L Sbjct: 1038 AVADPDEREALFARM-IEGAYRRGRALNMASHLEIDAVIDPADTRHWLLRGL------AS 1090 Query: 535 ALPAKKHGNIP 545 ALPA + P Sbjct: 1091 ALPASAARDTP 1101 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: 1424 Number of extensions: 71 Number of successful extensions: 7 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: 1112 Length adjustment: 41 Effective length of query: 505 Effective length of database: 1071 Effective search space: 540855 Effective search space used: 540855 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: 55 (25.8 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