Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate CCNA_02250 CCNA_02250 methylcrotonyl-CoA carboxylase biotin-containing subunit
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__Caulo:CCNA_02250 Length = 654 Score = 478 bits (1230), Expect = e-139 Identities = 288/689 (41%), Positives = 394/689 (57%), Gaps = 62/689 (8%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 M +LIANRGEIA R+I+TAR++G++T+AVYS+AD NA V AD AI IGP PA +SY Sbjct: 1 MLSSVLIANRGEIARRIIRTARELGVRTIAVYSEADANAPFVMEADAAILIGPAPAKESY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + KI+ A + GAEA+HPGYGFLSE +FA ++ AG+V+IGPP AI AMG K +K Sbjct: 61 LDPRKILAAARQMGAEAIHPGYGFLSENAEFAQSVIDAGLVWIGPPPSAIRAMGLKDAAK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 + +AGV T PGY+G + + +IGYPV+IKA AGGGGKGMR + + Sbjct: 121 AVMIKAGVPTTPGYLGEDQSVERLTVEAAKIGYPVLIKAVAGGGGKGMRKVERAEDFEAA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 S + EA+ +FGDDR+ +EK+VT+PRHIE+QV D HGN V+L ER+CS+QRR+QKVIE Sbjct: 181 LGSCRREASAAFGDDRVLLEKYVTRPRHIEVQVFGDSHGNVVHLFERDCSLQRRHQKVIE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQK-----NFYFLEMNTRLQV 295 EAP+P +DEATR+A+ A A+AV Y AGTVEFI D + +F+EMNTRLQV Sbjct: 241 EAPAPGMDEATREAVCAAAVKAAQAVNYVGAGTVEFIADASEGLRADRIWFMEMNTRLQV 300 Query: 296 EHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRL 355 EHPVTE++TG DLVE +RVA+GE LP +Q ++ ++GWAME+RLYAE+P FLPS G+L Sbjct: 301 EHPVTEMVTGQDLVEWQLRVASGEPLPLEQDEITLDGWAMEARLYAENPATGFLPSTGKL 360 Query: 356 TRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTF 415 +R P VR D+ V EGGE++ +YDPMIAKL RE A + + A Sbjct: 361 KHFR------LPEGDVRVDSAVEEGGEVTPFYDPMIAKLIAHGADREDAAQRLAEACALV 414 Query: 416 EVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMN 475 EV + N F+ HP FV G + T FI + + A DEP + + + Sbjct: 415 EVWPVKTNAAFLAKCASHPDFVDGAVDTGFIEARLDELTERAFSDEPAMAAIGWRLDSFL 474 Query: 476 RVAEIRR-------TRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGS-----TVS 523 AE RR +++ G N R + ++ G++ + +A G+ + Sbjct: 475 E-AEARRDPWEGAPSKLLGFRMNAPR-ASMHLPMSTDGKATPLRVALIGGGTEDWSWDIR 532 Query: 524 FSDGSS------LRVTSDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVR 577 +DGS+ L T P Q V V K+G G GA Sbjct: 533 HADGSTFDEVTRLPTTYGKGPIQVFEGGDVQEFDFVAKIGGAGEG------GA------- 579 Query: 578 TPRQAELALLMPEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENIL 637 + +L PMPG +V ++V+ G V +GQ L T+EAMKME+ + Sbjct: 580 ------------------SDGAILSPMPGKIVSVSVSAGQTVSKGQTLLTLEAMKMEHAM 621 Query: 638 RAERRGTVKKIAAAPGASLRVDDVIMEFE 666 A G V +++A G + V+ E Sbjct: 622 AAPFDGVVAELSAVAGGQVSEGVVLARLE 650 Lambda K H 0.318 0.134 0.386 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: 1119 Number of extensions: 57 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: 666 Length of database: 654 Length adjustment: 38 Effective length of query: 628 Effective length of database: 616 Effective search space: 386848 Effective search space used: 386848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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