Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate AO353_19305 AO353_19305 3-methylcrotonyl-CoA carboxylase
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19305 Length = 653 Score = 492 bits (1266), Expect = e-143 Identities = 278/671 (41%), Positives = 398/671 (59%), Gaps = 29/671 (4%) Query: 3 KKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYIV 62 +KILIANRGEIACR+ +TA+ +G +TVAV+SDAD +ALHV MADEA++IGP QSY+ Sbjct: 5 RKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVRMADEAVNIGPAAVAQSYLN 64 Query: 63 IDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKKL 122 I++A SGA+A+HPGYGFLSE +FA A AG+ FIGP AIE MG K SK Sbjct: 65 SAAIIDAALRSGADAIHPGYGFLSENAEFATACAQAGITFIGPDPAAIELMGSKRLSKIA 124 Query: 123 AKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGFE 182 AGV + GY G D + + IGYP+MIKASAGGGG+GMR+ + E+ Sbjct: 125 MLAAGVPCIGGYQGAEQDDATLSREAERIGYPLMIKASAGGGGRGMRLVHTADELLAQIR 184 Query: 183 SSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEEA 242 ++++EA ++FG D + +E+ + +PRH+EIQ+ D+HGN +YL ER+CSIQRR+QKVIEEA Sbjct: 185 TARSEALHAFGSDELILEQALIEPRHVEIQLFGDQHGNLIYLGERDCSIQRRHQKVIEEA 244 Query: 243 PSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTEL 302 P P + R AMGE A +AV Y AGTVEF++D + FYFLEMNTRLQVEHPVTE+ Sbjct: 245 PCPVMTAELRDAMGEAALKAGRAVNYVGAGTVEFLLDARGQFYFLEMNTRLQVEHPVTEM 304 Query: 303 ITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRPPV 362 ITG+DLV + VAAG LP +Q +++ G AME RLYAEDP ++FLP GR+ R+ P + Sbjct: 305 ITGLDLVAWQLDVAAGLPLPLRQEQVELKGHAMEVRLYAEDPAQDFLPQTGRIMRWEPAL 364 Query: 363 ESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGIGH 422 VR D G+ EG ++S +YDP++ K+ + TRE A ++ A+ + G+ Sbjct: 365 -----ADGVRIDHGLLEGQQVSPFYDPLLGKIIAYGATREEARRKLLRAVQDSALLGLQT 419 Query: 423 NLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAM-NRVAEIR 481 N + +++HP+F+ GD T FIA+ + D PT +A A A + A Sbjct: 420 NQRLLAGLLEHPQFIAGDFNTGFIAQHFAD-HPSLHSHAPTAEELAIATALFYQQSAGAH 478 Query: 482 RTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSDWTPGQP 541 ++G NN + + + L G+ + + A +G V G +L+ Sbjct: 479 PPGLAGWRNN--ANAPLLQQIGLNGDRWSTEVTALPDGQLVIQVAGETLQ---------- 526 Query: 542 LASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPDTSKY-- 599 L L ++ R +++ I + +L L + R LL + L P +S+ Sbjct: 527 LKLLDINARSANLEINGIRRRYAYQLAAGQLWLFTRPGS----LLLQDQTLAPVSSQVGT 582 Query: 600 ----LLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGAS 655 L PM G +V + V+EG V +GQ L +EAMKME+ L+A G +K++ +PG Sbjct: 583 STGTLKAPMDGAIVDVLVSEGSSVTKGQLLLVLEAMKMEHPLKAGIDGVIKRLQVSPGDQ 642 Query: 656 LRVDDVIMEFE 666 ++ +++E E Sbjct: 643 VKNRQILLEVE 653 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: 1001 Number of extensions: 40 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: 653 Length adjustment: 38 Effective length of query: 628 Effective length of database: 615 Effective search space: 386220 Effective search space used: 386220 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