Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate N515DRAFT_0927 N515DRAFT_0927 3-methylcrotonyl-CoA carboxylase alpha subunit
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__Dyella79:N515DRAFT_0927 Length = 665 Score = 499 bits (1285), Expect = e-145 Identities = 299/679 (44%), Positives = 393/679 (57%), Gaps = 30/679 (4%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF+++LIANRGEIACRVI+T R++GI+T+AVYS+AD +A HV +ADEA IG P SY Sbjct: 1 MFERVLIANRGEIACRVIRTCRRLGIRTIAVYSEADADAQHVRLADEAWPIGGPRPADSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + + I+E + SGA+A+HPGYGFLSE FA A AG+ FIGP +I+AMG K +K Sbjct: 61 LRGETILEVARRSGAQAIHPGYGFLSENTAFARACTEAGIAFIGPRPASIDAMGSKAAAK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 L ++ V VPGY G DAD + G+P+MIKA+AGGGGKGMRI +E E + Sbjct: 121 ALMEKHAVPLVPGYHGDNQDADFLAGQARSTGFPLMIKAAAGGGGKGMRIVRAEREFADA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 S++ EAAN+FGD R+ +E++V PRHIE QV D HGN ++L+ERECS QRR QKV+E Sbjct: 181 LASAQREAANAFGDTRVILERYVEHPRHIEFQVFGDTHGNVIHLNERECSAQRRYQKVLE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 E PSPFL A R AMG A A A+AV Y AGTVEFIV F+F+EMNTRLQVEHPVT Sbjct: 241 ETPSPFLTPARRAAMGAAAVAAARAVDYVGAGTVEFIVGQDGEFFFMEMNTRLQVEHPVT 300 Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360 E G+DLVE +RVAAGE LP +Q D+ G A+E RLYAEDP +NFLP G+L R R Sbjct: 301 EETLGLDLVEWQLRVAAGEALPLRQEDVHAQGHAIEVRLYAEDPEQNFLPGSGKLLRLRL 360 Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420 P S VR D GV EG ++++YDPMIAKL R A++ +R AL E+ G Sbjct: 361 PETS----RHVRLDGGVIEGDTVTIFYDPMIAKLIVHDRDRAQALQRLREALMACEIAGP 416 Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480 N+ F+ ++ HP V+G I T ++ + G P L AA AA ++ + Sbjct: 417 KSNIAFLERLVRHPVVVEGRIDTGYLDRHLDEFLAGDAAPAPQLLFAAAVAALLHDERTV 476 Query: 481 RRTRISGTMNNHERHVGVD-W----------VVALQGESYHVSIAADREGSTVSFSDGSS 529 G ++ H D W ++L+ + Y V A +G +S Sbjct: 477 VAQAAHG-VDPHSPWARADAWRIGHAGKRIVALSLREQRYEVE-AHGHDGDYQLCHGDAS 534 Query: 530 LRVTSDWTPGQPLASLMVDGRPLVMKVGKIPM---GFRLRLRGADLKVNVRTPRQAELAL 586 V G L S DG+ L ++P+ R+ L +D R A A Sbjct: 535 CHVQGARHDGAAL-SARFDGQSL-----RLPLHADAQRVLLHDSD----GRRHSFARAAA 584 Query: 587 LMPEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVK 646 E +L PMPG +V + GD+V+EGQ L +EAMKME L+A R GT+ Sbjct: 585 FAWEARQGAGGNQVLAPMPGRIVLVKARPGDQVEEGQELLVMEAMKMELALKAPRAGTID 644 Query: 647 KIAAAPGASLRVDDVIMEF 665 I A G + D V++ F Sbjct: 645 SIGATQGDFVEADAVLVRF 663 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: 1118 Number of extensions: 50 Number of successful extensions: 4 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: 665 Length adjustment: 38 Effective length of query: 628 Effective length of database: 627 Effective search space: 393756 Effective search space used: 393756 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