Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF1016 PGA1_c10330 methylcrotonoyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__Phaeo:GFF1016 Length = 645 Score = 483 bits (1243), Expect = e-140 Identities = 305/684 (44%), Positives = 391/684 (57%), Gaps = 61/684 (8%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF KILIANRGEIACRV++TAR MG++TVAVYSDAD A HV MADEA+HIG SY Sbjct: 1 MFDKILIANRGEIACRVMETARAMGVRTVAVYSDADVTAKHVQMADEAVHIGGSAPADSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + D I+ + SGA+A+HPGYGFLSE F A+EAAG+ FIGP + AI MG K +K Sbjct: 61 LKGDVIIRVAQESGAQAIHPGYGFLSENPAFVDAVEAAGLSFIGPSADAIRKMGLKDAAK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 L ++AGV VPGY G DA+ + +IGYPV+IKA AGGGGKGMR+ + AE + Sbjct: 121 ALMEKAGVPVVPGYHGANQDAEFLAGEAEKIGYPVLIKAVAGGGGKGMRLVEAPAEFSDA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 +S++ EA +FG+ + IEK++ QPRHIE+QV D + V+L ER+CS+QRR+QKVIE Sbjct: 181 LKSAQGEATTAFGNPDVLIEKYIQQPRHIEVQVFGD-GTHAVHLFERDCSLQRRHQKVIE 239 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQ-----KNFYFLEMNTRLQV 295 EAP+P + R+AMGE A+A+GY AGTVEFIVDG F+F+EMNTRLQV Sbjct: 240 EAPAPGMTAEMREAMGEAGVRAAEAIGYKGAGTVEFIVDGSDGLRTDGFWFMEMNTRLQV 299 Query: 296 EHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRL 355 EHPVTELITG+DLVE +RVA+GE LP QQ DL I G A E+RLYAED + FLP+ G L Sbjct: 300 EHPVTELITGVDLVEWQLRVASGESLPAQQDDLTITGHAFEARLYAEDVPKGFLPATGTL 359 Query: 356 TRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTF 415 T P E R D+GV G IS +YDPMI+K+ TR A+ ++R AL+ Sbjct: 360 THLSFPAE-------CRADSGVRAGDTISPWYDPMISKVIVHGATRSVALSKLRRALERT 412 Query: 416 EVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMN 475 EV G NL F+GA+ H F +G++ T IA + AV D P +AAA A+ Sbjct: 413 EVAGTVTNLAFLGALASHQGFGRGEVDTGLIARDLE--ALTAVGDMPVAHWIAAAQRAL- 469 Query: 476 RVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVS--FSDGSSLRVT 533 SG + + V L + I + G D SS VT Sbjct: 470 ------CLHKSGGDSGFTLWAPLHRAVQLTHGEESLEITVEVLGPQAQRWQLDDSSHEVT 523 Query: 534 SDWT----PGQPLASLM-VDGRPLVM-KVGKI-----PMGFRLRLRGADLKVNVRTPRQA 582 D T G PL ++ DGR V ++ I P+ R G D V Sbjct: 524 FDGTCWRHDGHPLPNVAEADGRLTVFARISSIFDCIDPLD-RAGTAGGDTNV-------- 574 Query: 583 ELALLMPEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERR 642 + PMPGLV + G EV+EG LA +EAMKME+ L A R Sbjct: 575 -----------------IEAPMPGLVKAVFAEAGAEVKEGDRLAILEAMKMEHSLLAARD 617 Query: 643 GTVKKIAAAPGASLRVDDVIMEFE 666 G V ++ A+ G + ++ E Sbjct: 618 GVVAEVLASAGDQVEAGAALVRLE 641 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: 1079 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 666 Length of database: 645 Length adjustment: 38 Effective length of query: 628 Effective length of database: 607 Effective search space: 381196 Effective search space used: 381196 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