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_053544274.1 CDES_RS03395 pyruvate carboxylase
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_001277995.1:WP_053544274.1 Length = 1140 Score = 379 bits (974), Expect = e-109 Identities = 222/523 (42%), Positives = 315/523 (60%), Gaps = 21/523 (4%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARA-ADSY 60 F K+LVANRGEIAVR RA E G TVA+Y D+ H +A EA IG + +Y Sbjct: 12 FKKILVANRGEIAVRAFRAAYETGAATVAIYPREDRGSFHRSFASEAVRIGQEGSPVKAY 71 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 LD + +I AA+K ADAI+PGYGFL+ENA+ AR+ ++ T++GP+ + ++ G+K++A Sbjct: 72 LDIDEIIGAAKKVKADAIYPGYGFLSENAQLARECAENGITFIGPTPEVLDLTGDKSRAV 131 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + ++A +PV+ +T P+ S +D+ A+ YP+ +KA GGGGRG++ V +++ Sbjct: 132 TAAKEAGLPVLAEST-PSRSIDDIVKSAEGQTYPIFVKAVAGGGGRGMRFVEKPEDLRKL 190 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 A RE EA F + +VYVE+ + P+HIEVQIL D G+V HL ERDCSLQRRHQKV+E Sbjct: 191 ATEASREAEAAFGDGAVYVERAVINPQHIEVQILGDHTGDVIHLFERDCSLQRRHQKVVE 250 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV-EDGEFYFMEVNTRIQVEHTVT 299 AP+ L +LR+RI A + R+ Y AGTVEFLV E G F+E+N RIQVEHTVT Sbjct: 251 IAPAQHLDPELRDRICADAVKFCRSIGYQGAGTVEFLVDEKGNHVFIEMNPRIQVEHTVT 310 Query: 300 EEVTGLDVVKWQLRVAAG---EELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLST 356 EEVT +D+VK Q+R+AAG ++L +QD ++ G +++ RI E P F P TGT++ Sbjct: 311 EEVTEVDLVKAQMRLAAGATLKDLGLTQDKIKTHGAALQCRITTEDPNNGFRPDTGTITA 370 Query: 357 YDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRT 416 Y PGG G+R+D A + G EI +DSM+ K+ GSD + RA+RAL EF + G+ T Sbjct: 371 YRSPGGAGVRLDGAAQLGGEITAHFDSMLVKMTCRGSDFATAVARAQRALAEFTVSGVAT 430 Query: 417 VIPFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEVTERTFT 476 I F R +L +E F T ++ + P ++A P A D+E+G + + Sbjct: 431 NIGFLRALLREEDFTTKRIATGFIAD--HPHLLQA------PPA---DDEQGRILDYLAD 479 Query: 477 VEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREE 519 V VN E + A PL A P G R R ++ Sbjct: 480 VTVNKPHGERPKD----IAAPLDKLPAIKDLPLPRGSRDRLKQ 518 Score = 57.0 bits (136), Expect = 4e-12 Identities = 37/106 (34%), Positives = 56/106 (52%), Gaps = 5/106 (4%) Query: 499 GGASAAASASKPSGPRKRREESDEGGQQVIEGDGES----VAAEMQGTILAVEVDEGDDV 554 G + A+ + P + R+ S E E S VAA G ++ V V EGD+V Sbjct: 1035 GMRNVVANVNGQIRPMRVRDRSVESVTATAEKADPSNKGHVAAPFAG-VVTVTVAEGDEV 1093 Query: 555 EPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVLLVL 600 + GD V I+EAMKME + A GT+ +V+V V+ GD+++V+ Sbjct: 1094 KAGDAVAIIEAMKMEATITAHADGTIQRVVVPAATKVEGGDLIVVI 1139 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: 1406 Number of extensions: 58 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: 1140 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1098 Effective search space: 613782 Effective search space used: 613782 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