Align propionyl-CoA carboxylase β subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_4479 Biotin carboxylase (EC 6.3.4.14)
Query= metacyc::MONOMER-17284 (514 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4479 Length = 1095 Score = 212 bits (540), Expect = 5e-59 Identities = 157/512 (30%), Positives = 241/512 (47%), Gaps = 32/512 (6%) Query: 4 PEEQLATLFRLRER---ALQGGGPERVAQQHARGKLTARERLALLLDPNSFQEIGALASS 60 P+ A L R+ +R PE +A++HA+G TARE +A L D SF E GALA + Sbjct: 579 PDHIRADLQRVIDRHAFTFDAARPEAIAKRHAQGGRTARENIADLCDNGSFIEYGALAIA 638 Query: 61 PLG------DEDQRVPGDGIVTGFGKINGR-------RVAVFAQDFTVMGGSFSAVQANK 107 D P DG+VTG G ING R V + D TV+ G+ A K Sbjct: 639 AQARRRSKEDLIANTPADGMVTGIGGINGALFGDEKSRAVVMSYDATVLAGTQGARNHAK 698 Query: 108 ICRMQDLAIESGIPIIGLNDSGGARIQEGVRSLAA--YGEVFVRNVMASGVVPQISAILG 165 RM +A+ +P++ + GG R + + A + F SG VP I G Sbjct: 699 TDRMLGIALAQKLPVVLFAEGGGGRPGDTDMPIVAGLHVHTFASYAALSGQVPVIGIAAG 758 Query: 166 PCAGGAVYSPALTDFVIMSESTGYMFLTGPDVIKAVSGRELSTQELGGAAVHCVRSGVAH 225 C G +D +I + + + + GP +I+ +++G + V +GV Sbjct: 759 RCFAGNAALLGCSDVIIATRGSN-IGMGGPAMIEGGGLGVFKPEQIGPSRVQHA-NGVID 816 Query: 226 LSAADDRAVIELIKRLLSYLPQNNNEDPPQIMPYDRADRIEPALNSLVPADERQGYDIHT 285 + D+ ++ + LS+ P P R L ++VP + + YD T Sbjct: 817 VLVDDEAGAVQAARHYLSFF---QGRTPEWSAPDQRL------LRAVVPENRLRVYDTRT 867 Query: 286 LINLICDYDSFLEIQPLFAPNAVVGFARLDGYAVGIVANQPAVMAGALDIDASDKIARFV 345 + + D S L ++ F AR++G VG++AN P + GA+D DA+DK ARF+ Sbjct: 868 AMAGLVDDASLLPLRTGFGAGIHTALARIEGRPVGLLANNPQHLGGAIDADAADKGARFM 927 Query: 346 RICDAFNIPLITFVDTPGFLPGVEQEYGGVIRHGAKIIYAYSEATVPKISVVVRKAIGGA 405 ++C+A +P+++ VDTPGF+ G E E +RH +++ + VP SVV+RK G Sbjct: 928 QLCNAHGLPIVSLVDTPGFMVGPEVEATAQVRHVSRLFVTAASLRVPTFSVVLRKGYGLG 987 Query: 406 YVAMSSKQLRCDL-NFAWPSAQIAVMGAEGAVRILRREELRTAENPAQLMEQFIADYRRR 464 + M++ + AWP+ + MG EGAVR+ R+EL A+ F + Sbjct: 988 AMGMTAGGFHAPVFTVAWPTGEFGAMGLEGAVRLGFRKELEALPEGAERDALFAKLLAKS 1047 Query: 465 YFN--PYHAADLGQIDEVIEPAETRPRLIRAL 494 Y N H A +ID VI+PA+TR L R L Sbjct: 1048 YANGEAMHMAATLEIDAVIDPADTRAWLARGL 1079 Lambda K H 0.321 0.138 0.400 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: 1402 Number of extensions: 64 Number of successful extensions: 8 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: 514 Length of database: 1095 Length adjustment: 40 Effective length of query: 474 Effective length of database: 1055 Effective search space: 500070 Effective search space used: 500070 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: 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