Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011383117.1 AMB_RS03465 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000009985.1:WP_011383117.1 Length = 665 Score = 528 bits (1359), Expect = e-154 Identities = 316/677 (46%), Positives = 415/677 (61%), Gaps = 26/677 (3%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF KILIANRGEIACRV++TA+++GI+TVAVYS+AD NA+HV+MADEA+ IGP A +SY Sbjct: 1 MFDKILIANRGEIACRVMRTAKRLGIRTVAVYSEADANAMHVAMADEAVLIGPAAAAESY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + D I+EA K +GA+A+HPGYGFLSE FA A AGVVFIGPP GAI AMG K SK Sbjct: 61 LKGDVILEAAKRTGAQAIHPGYGFLSENAGFAEACAKAGVVFIGPPVGAIHAMGSKAESK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 +L + AGV VPGY G +E + + IGYPV++KASAGGGGKGMR+ + + E Sbjct: 121 RLMEAAGVPLVPGYHGKGQTLEELTREAAIIGYPVLVKASAGGGGKGMRVVSEASGLAEA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 S+K EA +FGDD + +E ++ +PRH+EIQV D HGN VYL ER+CSIQRR+QKVIE Sbjct: 181 VASAKREAKAAFGDDSLLLETYLGRPRHVEIQVFCDTHGNGVYLFERDCSIQRRHQKVIE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIV-DGQKNFYFLEMNTRLQVEHPV 299 EAP+P L + TR+AMGE A A A+AV Y AGTVEF+ DG+ F+F+EMNTRLQVEHPV Sbjct: 241 EAPAPALADETRRAMGEAAVAAAQAVDYVGAGTVEFLYQDGR--FFFIEMNTRLQVEHPV 298 Query: 300 TELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYR 359 TE+ITG+DLVE + VA+G KLP Q L G A E+RLYAEDP R+FLP+IG+L Sbjct: 299 TEMITGLDLVEWQLLVASGGKLPLAQEQLSRKGHAFEARLYAEDPSRDFLPAIGKLVHLA 358 Query: 360 PPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEG 419 PP E+ VR DTGV +G +++ +YDPMIAKL W R++A+ +R AL ++V G Sbjct: 359 PPSEN----RHVRVDTGVRQGDQVTPFYDPMIAKLIVWDEDRDSALRRLRRALADYQVAG 414 Query: 420 IGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTL-RRVAAAAAAMNRVA 478 + N+ F+GA+ HP F +I T FI E Y Q P + A+ A + R Sbjct: 415 VTTNVSFLGAIAAHPAFAALEIDTGFI-ERYRADLQPPAAPVPAMGLAFASLALLLWREE 473 Query: 479 EIRRTRISGTMNNHERHVGVDWVVALQGESYH---VSIAADREGSTVSF-SDGSSLRVTS 534 + RT + H W L +++H AD TV F +DG SL + Sbjct: 474 DSARTAARSGDPHSPWHQTNGW--RLNDDNHHDFRFMDGADERRVTVHFVADGWSLDL-- 529 Query: 535 DWTPGQPLAS--LMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKL 592 P Q L++ + G L ++G + G D+ V + ++ L P Sbjct: 530 ---PDQTLSARRATLSGTTLSAEIGGERRTASVVRSGFDITV-LHDGHAWKIKLDDPSAT 585 Query: 593 PPDT---SKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIA 649 + L PMPG VV++ V GD V GQ L VEAMKME+ ++A G V I Sbjct: 586 AAEREGGDGRLAAPMPGTVVQVLVQPGDAVTAGQPLIVVEAMKMEHAIKAPAEGKVAAIH 645 Query: 650 AAPGASLRVDDVIMEFE 666 G ++ ++ FE Sbjct: 646 FKVGDTVAEGVELLAFE 662 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: 1122 Number of extensions: 47 Number of successful extensions: 4 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: 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