Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate CA265_RS16635 CA265_RS16635 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::Q3J4E3 (510 letters) >FitnessBrowser__Pedo557:CA265_RS16635 Length = 513 Score = 643 bits (1659), Expect = 0.0 Identities = 316/500 (63%), Positives = 390/500 (78%), Gaps = 5/500 (1%) Query: 15 ARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCTDFGMQDDRPAGDGV 74 A GGGQ R+++QHK+GKLTARERI L+DEGSFEE M V HR TDFGM+ ++ GDGV Sbjct: 15 ANLGGGQARIDSQHKKGKLTARERIHFLMDEGSFEEIGMMVTHRSTDFGMEREKYLGDGV 74 Query: 75 VTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGAPVIGLNDSGGARIQ 134 VTG+GT++GR+ YVFSQDFTVFGGSLSETHA+KICK+MDMAM+NGAP+IGLNDSGGARIQ Sbjct: 75 VTGYGTVSGRLTYVFSQDFTVFGGSLSETHAEKICKLMDMAMKNGAPLIGLNDSGGARIQ 134 Query: 135 EGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDFIFMVRDTSYMFVTG 194 EGV SL GYAD+F +N+ ASGVIPQ+S IMGPCAGGAVYSPA+TDFI MV +TSYMFVTG Sbjct: 135 EGVVSLGGYADIFYKNVQASGVIPQLSAIMGPCAGGAVYSPAITDFILMVENTSYMFVTG 194 Query: 195 PDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRRLVDFLPLSNRTPAP 254 P+VVKTVT+E VT+EELGGASTH KS V A N++EA+ +++L+ ++P + A Sbjct: 195 PNVVKTVTHEEVTSEELGGASTHATKSGVTHFACANEIEAINHLKKLLSYMPQNCEEIAD 254 Query: 255 VRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQKDFAANIITGFIRL 314 P ++ L+T +P+N +QPYD++E+I +AD F E+ +A NI+ GF RL Sbjct: 255 HLP-YETADESRPELNTFMPENASQPYDIREVISAVADTDSFLEVHAAYAENIVVGFARL 313 Query: 315 EGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVDVPGFLPGTGQEYGG 374 G+++G+VANQP LAG LD +SS KAARFVRFCD FNIP+L DVPGFLPGT QE+ G Sbjct: 314 AGRSIGIVANQPAYLAGVLDSNSSTKAARFVRFCDCFNIPLLVFEDVPGFLPGTDQEWNG 373 Query: 375 VIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNYAWPTAEIAVMGAKG 434 +I +GAKLL+A+ EATVP++TVITRKAYGGAYDVM SKH+ D NYAWP+AEIAVMGAKG Sbjct: 374 IITNGAKLLYAFSEATVPRITVITRKAYGGAYDVMNSKHIGADMNYAWPSAEIAVMGAKG 433 Query: 435 ATEILYRSELGD----KEKIAARAKEYEDRFANPFVAAERGFIDEVIMPHSTRRRVSKAF 490 A EI+++ E+ +EK + K Y D FANP+ AAERGF+DEVI P TR ++ KAF Sbjct: 434 AAEIIFKREITSAEKPEEKWLEKEKLYSDIFANPYRAAERGFVDEVIEPAQTRIKLIKAF 493 Query: 491 ASLRNKKLANPWKKHDNIPL 510 L NK + NP KKH NIPL Sbjct: 494 KMLENKVVNNPRKKHGNIPL 513 Lambda K H 0.321 0.138 0.404 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: 785 Number of extensions: 27 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: 510 Length of database: 513 Length adjustment: 35 Effective length of query: 475 Effective length of database: 478 Effective search space: 227050 Effective search space used: 227050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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