Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_013258314.1 DEBA_RS07480 carboxyl transferase
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_000143965.1:WP_013258314.1 Length = 520 Score = 294 bits (753), Expect = 5e-84 Identities = 171/511 (33%), Positives = 272/511 (53%), Gaps = 15/511 (2%) Query: 1 MTMEDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHR 60 M E +++L+++RE AL GG ++ Q+D GK AR+RI LD +F E Sbjct: 1 MAFEKELEQLQKRRERALAMGGPAKLQRQYDAGKYDARQRIQRLLDADSFMEIGML---- 56 Query: 61 NHKF--GMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAM 118 NH GME+ K P D I G G++DGR V + A+DFTV + + K + + Sbjct: 57 NHSDVPGMEQ-KTPADSKIGGFGKIDGRWVAIAANDFTVMAATSSRIAGRKEGHLKHHSA 115 Query: 119 EVGAPVIGLNDSAGARIQE--GVQSLGGFG----EIFRRNTEASGVVPQISAIMGPCAGG 172 G P+I L ++ GAR+ + G Q L FG + + + P ++A+MG C G Sbjct: 116 AHGMPLIYLGEAGGARMPDIMGSQGLASFGGGDLDSYLKIMSRVRQSPMVAAVMGECYGM 175 Query: 173 AVYSPALTDFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDT 232 + L DF V+ ++ M ++GP +++ GE+ T +ELGG H +G+A + Sbjct: 176 PTWMACLADFVVQVKGSA-MGVSGPRILEIALGEKTTDEELGGWKVHAEVTGMADRTVEN 234 Query: 233 EEQALDDIRHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGV 292 E++ IR L YLP + + PP VE + ++ +I+P+ + YD+H +LN V Sbjct: 235 EDECFAVIRQFLGYLPSHREQLPPVVETPAGSGQGMAKILDILPEARNRAYDMHRILNCV 294 Query: 293 LDEGSFFGVQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDS 352 +DEGS F ++ F +N++ R+ G SVG+VANQP AG +D + +K F+ CDS Sbjct: 295 VDEGSLFPLKPMFGRNVITALARIGGKSVGLVANQPMFGAGAMDTDGIDKVISFLCLCDS 354 Query: 353 FNIPILSFVDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMA 412 FN+P++ F D PGFL G E + + A + +VP +++I RK YG A+ M Sbjct: 355 FNVPLIFFHDTPGFLVGKAAERKRVGARVMNFMNALGQLSVPRLSIIVRKTYGMAFWNMM 414 Query: 413 SKHLGADVNYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYT 472 GAD AWPTAE++ + P+ A N+++ +L D+ D + + + + + A PY Sbjct: 415 GSGSGADFLVAWPTAEMSFVAPEIAANVVFGGKL-PQDERDKEKWQGMVDSMVDDATPYA 473 Query: 473 AADRGFVDDVIEPGDTRNRLIADLRMLKSKR 503 AA + DVI+P DTR ++ L + + R Sbjct: 474 AAGHHLIHDVIDPRDTREFIVKCLDICQDSR 504 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: 676 Number of extensions: 36 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: 516 Length of database: 520 Length adjustment: 35 Effective length of query: 481 Effective length of database: 485 Effective search space: 233285 Effective search space used: 233285 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