Align propionyl-CoA carboxylase β subunit (EC 6.4.1.3) (characterized)
to candidate 5210426 Shew_2867 pyruvate carboxylase, propionyl-CoA carboxylase (RefSeq)
Query= metacyc::MONOMER-17284 (514 letters) >FitnessBrowser__PV4:5210426 Length = 1094 Score = 234 bits (596), Expect = 2e-65 Identities = 160/515 (31%), Positives = 254/515 (49%), Gaps = 43/515 (8%) Query: 8 LATLFRLRERALQGGGPERVAQQHARGKLTARERLALLLDPNSFQEIGALASSPLGDE-- 65 LA F R++ L E VA++H+ GK TARE L LLD SF E G LA + + Sbjct: 581 LAEFFDRRDKTLDESRSEAVAKRHSEGKRTARENLNDLLDEGSFNEYGQLAIAAQRQKHA 640 Query: 66 -DQRV---PGDGIVTGFGKING-------RRVAVFAQDFTVMGGSFSAVQANKICRMQDL 114 D+ V P DG +TG G +N R AV + D+TVM GS V K R+ +L Sbjct: 641 IDKLVEISPADGKITGIGTVNADSFGEEAARCAVMSYDYTVMAGSQGLVNHKKTDRLLEL 700 Query: 115 AIESGIPIIGLNDSGGARIQE---------GVRSLAAYGEVFVRNVMASGVVPQISAILG 165 + +P++ + G R + + + ++ GE+ SG+VP + G Sbjct: 701 CKKWKLPLVIFAEGAGGRPSDTDYPGVAFLNLHTFSSLGEL-------SGLVPTVGIAAG 753 Query: 166 PCAGGAVYSPALTDFVIMSESTGYMFLTGPDVIKAVSGRELSTQELGGAAVHCVRSGVAH 225 C G + D I + + + GP +I+ +E+G +V +GV Sbjct: 754 NCFAGNAALYGVCDLTIATRQAS-IGMAGPAMIEGGGLGVFKPEEVGPPSV-LSPNGVID 811 Query: 226 LSAADDRAVIELIKRLLSYLPQNNNEDPPQIMPYDRADRIEPALNSLVPADERQGYDIHT 285 + D+ + + K+ LSY + +E + AD + L L+P + YDI Sbjct: 812 ILVEDEAEAVAVTKKYLSYFQGDLSE-------WQVAD--QRRLRHLIPENRMAIYDIRE 862 Query: 286 LINLICDYDSFLEIQPLFAPNAVVGFARLDGYAVGIVANQPAVMAGALDIDASDKIARFV 345 +I+ +CD DS LE++ FA N + R++G A G+ AN P + GA+D DA DK+ARF+ Sbjct: 863 VIDTLCDKDSVLELRREFAKNMITAMVRIEGKAYGLYANDPRFLGGAIDADAGDKLARFI 922 Query: 346 RICDAFNIPLITFVDTPGFLPGVEQEYGGVIRHGAKIIYAYSEATVPKISVVVRKAIGGA 405 ++CDA +IP+I+ DTPGF+ G E E +RH +++ + +TVP ++V+RK G Sbjct: 923 QLCDAHDIPMISLCDTPGFMVGPESEKRATVRHISRLFVHGANSTVPLFALVLRKGYGLG 982 Query: 406 YVAMSSKQLRCDL-NFAWPSAQIAVMGAEGAVRILRREELRTAENPAQLMEQFIADYRRR 464 + M+ + +WPS + MG EGAVRI + +L +P + F A + Sbjct: 983 VMGMTGGGFTAPVFTASWPSGEFGAMGIEGAVRIAAKRQLEAIADPDEREATFKAMVDKL 1042 Query: 465 YF--NPYHAADLGQIDEVIEPAETRPRLIRALEIL 497 Y + + A ++D VI+P E+R ++R L L Sbjct: 1043 YSHGSAINTASYLELDAVIDPMESRDWIVRGLACL 1077 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: 1265 Number of extensions: 67 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: 1094 Length adjustment: 40 Effective length of query: 474 Effective length of database: 1054 Effective search space: 499596 Effective search space used: 499596 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