Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012330372.1 M446_RS01880 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000019365.1:WP_012330372.1 Length = 671 Score = 787 bits (2033), Expect = 0.0 Identities = 414/671 (61%), Positives = 502/671 (74%), Gaps = 7/671 (1%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF KILIANRGEIACR+IKTAR+MGI+TVAVYSDADR+A+HV+MADEA+ IGP PA QSY Sbjct: 1 MFDKILIANRGEIACRIIKTARRMGIKTVAVYSDADRDAVHVAMADEAVAIGPAPAAQSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 +VI+KI+ A + +GA+AVHPGYGFLSER F AL AG+VFIGP GAI AMGDKI SK Sbjct: 61 LVIEKIIAACRQTGAQAVHPGYGFLSEREAFPKALAEAGIVFIGPNPGAIAAMGDKIESK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 K A A VSTVPG++G+I D AV+I++EIGYPVMIKASAGGGGKGMRIA S EV EG Sbjct: 121 KAASAAEVSTVPGFLGVIEDPAHAVRIADEIGYPVMIKASAGGGGKGMRIAHSAEEVAEG 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 F +++EAA+SFGDDR+F+EKF+T PRHIEIQV+ DKHGN +YL ERECSIQRRNQKVIE Sbjct: 181 FARARSEAASSFGDDRVFVEKFITDPRHIEIQVIGDKHGNVIYLGERECSIQRRNQKVIE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAPSP LDEATR+ MGEQA ALAKAV Y SAGTVEF+ K+FYFLEMNTRLQVEHPVT Sbjct: 241 EAPSPLLDEATRRKMGEQAVALAKAVNYDSAGTVEFVAGQDKSFYFLEMNTRLQVEHPVT 300 Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360 E+ITG+DLVE MIRVAAGE+LP Q+D+K+NGWA+ESR+YAEDP RNFLPSIGRLT YRP Sbjct: 301 EMITGLDLVELMIRVAAGERLPLSQADVKLNGWAVESRVYAEDPTRNFLPSIGRLTTYRP 360 Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420 P E + +RNDTGV EG EI+++YDPMIAKL +WAPTR AI ALD F ++GI Sbjct: 361 PAEGALGAATIRNDTGVEEGSEIAIHYDPMIAKLVSWAPTRAEAIGAQAQALDAFAIDGI 420 Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480 HN+PF+ A+M HPR+ +G ++T FIAEE+P GF+ R+AA AAA++ + Sbjct: 421 RHNIPFLSALMQHPRWQEGRLSTGFIAEEFPGGFEAPRPAGKVALRMAAVAAAIDHMLNE 480 Query: 481 RRTRISGTMNN--HERHVGVDWVVALQGESYHVSI----AADREGSTVSFSDGSSLRVTS 534 R+ ISG M + H R D VV L + + ++ AA + V+F+DG++ + S Sbjct: 481 RKRGISGQMRDPGHLRFER-DRVVWLGDQRFEATVETSAAAPVGATAVAFADGTTWPLES 539 Query: 535 DWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPP 594 DW PG P+ + + G ++V + G L+ GA + V T R+AELA LMP K Sbjct: 540 DWRPGDPVWTGTIGGARAAVQVRPLLNGVFLQHAGAAAEARVYTRREAELAALMPVKEVG 599 Query: 595 DTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGA 654 + K LLCPMPGLV I VA G EV+ G+ LA VEAMKMEN+LRAER TV+ I A G Sbjct: 600 GSGKQLLCPMPGLVKSIMVAPGQEVKAGEPLAIVEAMKMENVLRAERDATVQTIQAKEGD 659 Query: 655 SLRVDDVIMEF 665 SL VD VI+EF Sbjct: 660 SLAVDAVILEF 670 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: 1180 Number of extensions: 45 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: 666 Length of database: 671 Length adjustment: 38 Effective length of query: 628 Effective length of database: 633 Effective search space: 397524 Effective search space used: 397524 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 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