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_026608590.1 METAC_RS0121420 pyruvate carboxylase
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000427445.1:WP_026608590.1 Length = 1147 Score = 368 bits (945), Expect = e-106 Identities = 203/450 (45%), Positives = 275/450 (61%), Gaps = 11/450 (2%) Query: 4 KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAA-DSYLD 62 ++LVANR EI +RV RA ELG+RTVA+Y+E DK H ADEAY IG + ++YL Sbjct: 6 RLLVANRSEITIRVFRAATELGIRTVAIYAEEDKLSLHRFKADEAYQIGFGKGPLEAYLA 65 Query: 63 HESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSL 122 + VI AR+A DAIHPGYGFL+E+ EFA + ++GPS M LG K AR+L Sbjct: 66 IDDVIHIAREAKVDAIHPGYGFLSESPEFAEACAAAGIVFIGPSPQTMRALGNKVAARNL 125 Query: 123 MQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFE 182 VPV+P T D VK +A + GYPV +KA GGGGRG++ + SED++ Sbjct: 126 AVSCGVPVMPATPPLPDDPASVKRLAREIGYPVMLKASWGGGGRGMRPIESEDKLLEAVT 185 Query: 183 TAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEA 242 +AKRE ++ F VY+EK + RH+EVQIL D HG + HL ERDCS+QRR+QKV+E A Sbjct: 186 SAKREAKSAFGKDEVYLEKLVRRARHVEVQILGDAHGELVHLFERDCSIQRRNQKVVERA 245 Query: 243 PSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV--EDGEFYFMEVNTRIQVEHTVTE 300 P+P L E R + EAA + RA Y AGTVEFL+ E G FYF+EVN RIQVEHTVTE Sbjct: 246 PAPYLDEATRGALCEAALKIGRATGYVGAGTVEFLLDAESGGFYFIEVNPRIQVEHTVTE 305 Query: 301 EVTGLDVVKWQLRVAAGEELDF-------SQDDVEIEGHSMEFRINAEAPEKEFAPATGT 353 VTGLD+VK Q+R+A G+ + Q+++ + GH+++ RI E PE F P G Sbjct: 306 VVTGLDIVKAQIRIAEGKRIGRIEETGIPRQEEIRLSGHALQCRITTENPENNFIPDYGR 365 Query: 354 LSTYDPPGGIGIRMDDAVR-QGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIE 412 ++ Y G GIR+D G + YD ++ K+ + EE + R +RAL E+ I Sbjct: 366 ITAYRGAMGFGIRVDGGTAYSGAIVTRYYDPLLEKVTAWAATPEEAIRRMDRALLEYRIR 425 Query: 413 GLRTVIPFHRLMLTDEAFREGSHTTKYLDE 442 G+ T + F ++ F +TT+++DE Sbjct: 426 GVATNLAFLHNIINHPRFIANDYTTRFIDE 455 Score = 63.9 bits (154), Expect = 4e-14 Identities = 31/73 (42%), Positives = 45/73 (61%) Query: 529 EGDGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEG 588 EG+ V A M G + + V +G +V+ GD V LEAMKME + A R G +S++LV G Sbjct: 1075 EGNESHVGAPMPGAVSTIAVRQGQEVKAGDIVATLEAMKMETALHAPRDGKISEILVAPG 1134 Query: 589 DSVDMGDVLLVLE 601 +D D+L++LE Sbjct: 1135 QQIDARDLLMLLE 1147 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: 1350 Number of extensions: 65 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 601 Length of database: 1147 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1105 Effective search space: 617695 Effective search space used: 617695 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