Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_3016 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3016 Length = 675 Score = 507 bits (1306), Expect = e-148 Identities = 300/665 (45%), Positives = 388/665 (58%), Gaps = 20/665 (3%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MFKKILIANRGEIACRV TA+++G++TVAVYSDAD NA HV++ DEA+HIG SY Sbjct: 1 MFKKILIANRGEIACRVAATAQRLGVKTVAVYSDADANAKHVAVCDEAVHIGGSAPKDSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + ++I+EA KA+GA+A+HPGYGFLSE DFA A AAG+VFIGPP+ AI+ MG K SK Sbjct: 61 LRWERIIEAAKATGAQAIHPGYGFLSENEDFAQACAAAGLVFIGPPASAIKDMGLKAESK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 +L ++AGV VPGY G D + ++ IGYPV+IKASAGGGGKGMR + Sbjct: 121 QLMEKAGVPLVPGYHGSDQDPALLQREADRIGYPVLIKASAGGGGKGMRAVDKSEDFAAA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 ES K EA NSFGDD + +EK+V +PRHIEIQV D HGNCVYL ER+CS+QRR+QKV+E Sbjct: 181 LESCKREAINSFGDDAVLVEKYVQRPRHIEIQVFGDMHGNCVYLFERDCSVQRRHQKVLE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVD--------GQKNFYFLEMNTR 292 EAP+P + A R MGE A A AKAV Y AGTVEFIV+ Q FYF+EMNTR Sbjct: 241 EAPAPGMTPALRAQMGEAAVAAAKAVNYVGAGTVEFIVEQPGGYERPDQMKFYFMEMNTR 300 Query: 293 LQVEHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSI 352 LQVEHPVTE ITG+DLVE +RVA+GE LP QQ DL+I G A+E+R+ AE+P NFLP+ Sbjct: 301 LQVEHPVTEAITGLDLVEWQLRVASGEPLPLQQQDLRITGHAIEARICAENPDNNFLPAT 360 Query: 353 GRLTRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLAL 412 G L Y P +R D+GV +G IS +YD M+AKL TRE A+ + AL Sbjct: 361 GALNVYALPECVTFERGAIRVDSGVRQGDAISPFYDSMVAKLIVHGDTREQALARLDDAL 420 Query: 413 DTFEVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAA 472 + G+ N+ F+ V F + + TA I E F EP +AAAAA Sbjct: 421 AQTHIVGLATNVQFLRRVAKTDAFAQAKLDTALIPREQAVLFH----QEPVGLPLAAAAA 476 Query: 473 AMNRVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRV 532 + + R S ++ R G +Q + + + +++ G SL + Sbjct: 477 V---AQTLLKERASEGVDPFSRRDGFHTHGVVQ-RRFEFEFGGEHAKALLTYERGGSLHL 532 Query: 533 T----SDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLM 588 G + + DG L + + + + + + LL Sbjct: 533 AVGEGETAVAGPLVFAPQADGIELQFAGQRTRAAVYAQGEVDHVFTPLGATQITAIDLLA 592 Query: 589 PEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKI 648 L PMPG VV V GD V +GQ LA +EAMKME+ + A G V+++ Sbjct: 593 HAGEVAAEGGRLTAPMPGKVVSFAVKAGDTVAKGQPLAVMEAMKMEHTIAAPADGVVQEL 652 Query: 649 AAAPG 653 APG Sbjct: 653 LYAPG 657 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: 1120 Number of extensions: 49 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 2 Length of query: 666 Length of database: 675 Length adjustment: 39 Effective length of query: 627 Effective length of database: 636 Effective search space: 398772 Effective search space used: 398772 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