Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_089302466.1 CHB84_RS16245 pyruvate carboxylase
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_900188115.1:WP_089302466.1 Length = 1124 Score = 402 bits (1033), Expect = e-116 Identities = 222/448 (49%), Positives = 293/448 (65%), Gaps = 7/448 (1%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIG-PARAADS 59 MF KVLVANRGEIA+R RA ELG TVAV+ D++ H ADE++ IG P + Sbjct: 1 MFRKVLVANRGEIAIRAFRAGYELGAGTVAVFPHEDRNSLHRLKADESHQIGEPGHPVRA 60 Query: 60 YLDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKA 119 YL E V+ AA ADADA++PGYGFL+EN + AR E++ T+VGP A+ +E G K++A Sbjct: 61 YLSVEEVVRAALSADADAVYPGYGFLSENPDLARACEEAGITFVGPPAEILELTGNKSRA 120 Query: 120 RSLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179 ++A +PV+ G++ P+D +++ A A++ G+PV +KA GGGGRG++ V ++ Sbjct: 121 VQAAREAGIPVL-GSSRPSDDVDELVAAAEEIGFPVFVKAIAGGGGRGMRKVTEPAQLRE 179 Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239 E A RE E+ F + SV+VE+ + PRHIEVQILAD G V HL ERDCS+QRRHQKVI Sbjct: 180 SIEAASREAESAFGDPSVFVERAVVNPRHIEVQILADGTGEVVHLYERDCSVQRRHQKVI 239 Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV-EDGEFYFMEVNTRIQVEHTV 298 E AP+P L+ +LRERI A R R Y NAGTVEFLV E GE F+E+N RIQVEHTV Sbjct: 240 ELAPAPNLAPELRERICADAARLARRIGYRNAGTVEFLVDESGEHVFIEMNPRIQVEHTV 299 Query: 299 TEEVTGLDVVKWQLRVAAGE---ELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLS 355 TEEVT +D+V QLR+AAGE +L +QD + + G +++ RI E P EF P G +S Sbjct: 300 TEEVTDVDLVAAQLRIAAGESLADLGLTQDVIYLRGAALQCRITTEDPANEFRPDVGMIS 359 Query: 356 TYDPPGGIGIRMDDAVR-QGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGL 414 Y PGG GIR+D G EI +DSM+ KL G D + + RA RA+ EF I G+ Sbjct: 360 AYRSPGGSGIRLDGGTAFAGTEISAHFDSMLVKLTCRGRDFDTAVARARRAVAEFRIRGV 419 Query: 415 RTVIPFHRLMLTDEAFREGSHTTKYLDE 442 T IPF R +L D FR G TT ++++ Sbjct: 420 ATNIPFLRAVLDDPDFRAGRVTTSFIED 447 Score = 58.2 bits (139), Expect = 2e-12 Identities = 31/67 (46%), Positives = 43/67 (64%), Gaps = 1/67 (1%) Query: 535 VAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVDMG 594 VAA G ++ + V EGD VE G TV +EAMKME + A +GG VS++ + V+ G Sbjct: 1059 VAAPFAG-VVTLSVSEGDTVEAGATVATIEAMKMEAAITASKGGRVSRLAINSVQQVEGG 1117 Query: 595 DVLLVLE 601 D+LLV+E Sbjct: 1118 DLLLVVE 1124 Lambda K H 0.312 0.132 0.371 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: 1434 Number of extensions: 64 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 601 Length of database: 1124 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1082 Effective search space: 604838 Effective search space used: 604838 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 56 (26.2 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