Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_052300720.1 BTUS_RS06545 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_000092905.1:WP_052300720.1 Length = 508 Score = 615 bits (1586), Expect = e-180 Identities = 302/508 (59%), Positives = 381/508 (75%), Gaps = 1/508 (0%) Query: 9 ELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHKFGMEE 68 E+ E+R + GGG+ RIA QHD+GK+TARER++ LD GTFRE + F HR FG+++ Sbjct: 2 EMEERRRKVELGGGDRRIAQQHDRGKLTARERLEILLDPGTFRELNPFIEHRGTLFGLDK 61 Query: 69 TKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAPVIGLN 128 + PG+GV+TG+G+VDGRTV+VFA DFTVFGG+LGE+ A+KI K+MD A + G P+IGLN Sbjct: 62 VEAPGEGVVTGYGKVDGRTVYVFAQDFTVFGGALGEMHAQKIAKIMDLAAKSGCPIIGLN 121 Query: 129 DSAGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFTFMVRD 188 DS GARIQEGV SL G+G+IF RN+ SGVVPQIS IMGPCAGGAVYSPA+TDF FMV Sbjct: 122 DSGGARIQEGVVSLDGYGQIFYRNSIYSGVVPQISVIMGPCAGGAVYSPAITDFIFMVEG 181 Query: 189 TSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHLLSYLP 248 TS MFITGP VI+ VTGE ++ ++LGGA H SGVAHF EE+ L +R LLS+LP Sbjct: 182 TSQMFITGPKVIEAVTGESISSNDLGGAKVHGCLSGVAHFTGPGEEEVLGQVRRLLSFLP 241 Query: 249 QNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQEDFAKN 308 N+ E PPR +D + +E+ ++VP K YD+ V+ V+D+G F V FAKN Sbjct: 242 SNSREKPPRRSARED-DGWEEEMIDLVPVDGTKVYDVRRVIERVVDDGDFMEVHPQFAKN 300 Query: 309 IVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDVPGFLP 368 VVGF R+DG VGI+AN P+ AG LDI++S+K ARFIRFCDSFN+P+++F DV GF+P Sbjct: 301 AVVGFARIDGRPVGIIANNPKFMAGGLDIDSSDKIARFIRFCDSFNMPLITFEDVTGFIP 360 Query: 369 GTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYAWPTAE 428 G QEH GIIRHGAK+LYAYSEATVP +TVI RKA+GGAY + SK +GAD+ YAWP AE Sbjct: 361 GVKQEHGGIIRHGAKILYAYSEATVPKITVILRKAFGGAYVALNSKAIGADLVYAWPIAE 420 Query: 429 IAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVIEPGDT 488 +AVMGP+GA NI++ E+E + DP A R E I EYR F+NPY AA G VDDVI+P +T Sbjct: 421 VAVMGPEGAANIIFAREIEESPDPAATRAEKIAEYRARFSNPYVAASYGMVDDVIDPRET 480 Query: 489 RNRLIADLRMLKSKRKSQPDKKHGNIPL 516 R +L L +L+ K++S+P KKHGNIPL Sbjct: 481 RRKLKEALEILEEKQESRPAKKHGNIPL 508 Lambda K H 0.318 0.138 0.407 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: 844 Number of extensions: 43 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: 516 Length of database: 508 Length adjustment: 35 Effective length of query: 481 Effective length of database: 473 Effective search space: 227513 Effective search space used: 227513 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