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 YP_004134394.1 Mesci_6225 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000185905.1:YP_004134394.1 Length = 457 Score = 421 bits (1083), Expect = e-122 Identities = 216/447 (48%), Positives = 294/447 (65%), Gaps = 4/447 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF VL+ANRGEIA+R++RAC +LG++TVA +SEAD HV AD+A IGPA A +SY Sbjct: 1 MFDTVLIANRGEIALRILRACRDLGLKTVAAHSEADASLRHVALADKAICIGPAAATESY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ +I AA+ A AIHPGYGFL+ENA FA VE++ +VGPSA A+ +G+K A+ Sbjct: 61 LNIAEIIAAAQLTGAGAIHPGYGFLSENAAFAEAVENAGLIFVGPSATAIRTMGDKVSAK 120 Query: 121 SLMQDADVPVVPGTTE--PADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVD 178 M A VP V G+ P D E V+A+A+ GYPV +KA GGGGGRG+++V E + Sbjct: 121 RTMIAAGVPCVAGSEGALPQDEQE-VRAIAEAIGYPVIVKAAGGGGGRGMRIVRDEQALM 179 Query: 179 GQFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKV 238 A +E + F N VY+EK+LE PRHIE+QILAD+HG LGERDCS+QRRHQK+ Sbjct: 180 EAVSMAVKEADRAFGNPQVYLEKFLEQPRHIEIQILADKHGRAVWLGERDCSMQRRHQKI 239 Query: 239 IEEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTV 298 IEEAP+P ++ + IG+ R YT AGT EFL EDG F F+E+NTR+QVEH V Sbjct: 240 IEEAPAPGIAREAIGEIGDLCARACLTIGYTGAGTFEFLYEDGRFSFIEMNTRVQVEHPV 299 Query: 299 TEEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYD 358 TE VTG+D+V+ Q+R+A GE L FSQ+D+ I+GH++E RINAE P F P G + + Sbjct: 300 TELVTGIDIVREQIRIARGEPLSFSQEDIRIQGHAVECRINAEDP-YSFRPHPGRVERWT 358 Query: 359 PPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVI 418 PP G GIR++ + G + YDS++AKL+ G+ R E + R AL E + G+ T Sbjct: 359 PPSGPGIRVESHLYSGYTVPPHYDSLVAKLLAHGATRAEAIGRMRGALGEMEAVGIATNA 418 Query: 419 PFHRLMLTDEAFREGSHTTKYLDEVLD 445 P H +++ + F G +L+ +++ Sbjct: 419 PLHGILMEEPGFAAGGFDIHHLEHLIE 445 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: 650 Number of extensions: 24 Number of successful extensions: 3 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: 601 Length of database: 457 Length adjustment: 35 Effective length of query: 566 Effective length of database: 422 Effective search space: 238852 Effective search space used: 238852 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: 52 (24.6 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