Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011840850.1 RSPH17029_RS05950 biotin/lipoyl-binding protein
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000015985.1:WP_011840850.1 Length = 646 Score = 488 bits (1256), Expect = e-142 Identities = 291/676 (43%), Positives = 391/676 (57%), Gaps = 44/676 (6%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF+KILIANRGEIA R+ TAR++G+ TVAV+SDAD ALHV++ADEA+ IG P SY Sbjct: 1 MFRKILIANRGEIAVRIAATARRLGVATVAVHSDADAEALHVAVADEAVPIGGPQPADSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + ++++EA A+GAEA+HPGYGFLSE +F A+EAAG+VFIGP + AI AMG K +K Sbjct: 61 LRGERLIEAALATGAEAIHPGYGFLSENPEFVEAVEAAGLVFIGPSAAAIRAMGLKDAAK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 L EAGV VPGY G + + ++ +IGYPV+IKA AGGGGKGMR E Sbjct: 121 ALMAEAGVPVVPGYHGADQEPEHLALMAQDIGYPVLIKAVAGGGGKGMRRVERAEEFAAA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 S++ EA +FG++ + IEK++ PRHIE+QV D + V+L+ER+CS+QRR+QKVIE Sbjct: 181 LASARAEARTAFGNEAVLIEKWIDCPRHIELQVFGD-GTDAVHLYERDCSLQRRHQKVIE 239 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQ-----KNFYFLEMNTRLQV 295 EAP+P + R AMGE A A+A+GY AGTVEFIVDG F+F+EMNTRLQV Sbjct: 240 EAPAPGMTPGMRAAMGEAAVRAARAIGYRGAGTVEFIVDGSAGLSPDRFWFMEMNTRLQV 299 Query: 296 EHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRL 355 EHPVTE +TGIDLVE +RVAAGE LP Q D+ + G A E+RLYAED FLP+ GRL Sbjct: 300 EHPVTEAVTGIDLVEWQLRVAAGEPLPLAQKDIPLRGHAFEARLYAEDVPAGFLPATGRL 359 Query: 356 TRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTF 415 R +R DTGV G IS +YDPMIAK+ P+R +A+ + AL+ Sbjct: 360 DHLR-------FADGIRADTGVRTGDRISPWYDPMIAKIVAHGPSRASALNRLARALEET 412 Query: 416 EVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMN 475 EV G NL F+ + HP F G++ T I + A L T+ A Sbjct: 413 EVAGTVTNLAFLCRLAQHPGFAAGEVDTGLIGRDLAPLIAPATLAPETVAAALLVAELGE 472 Query: 476 RVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSD 535 A ++ + + H V L+ S ++ A E + + R+ + Sbjct: 473 TPAPLQGFSLWAPLRRH---------VRLRHGSEKIAAALTVEAPGRATVELGEARLAAR 523 Query: 536 WTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPD 595 P V+GRP R+ GA + V RT ++ +P+ L Sbjct: 524 LRP----EGWAVEGRPPA----------RVLRIGAQVHVFART---GTVSFEIPDPLDRG 566 Query: 596 TSK-----YLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAA 650 T + L PMPGLV +++V GD V++G LA +EAMKME++L A R GTV ++ Sbjct: 567 TEEAGQGGLTLSPMPGLVREVSVRAGDRVEKGDRLAVIEAMKMEHVLTAARDGTVAEVLV 626 Query: 651 APGASLRVDDVIMEFE 666 GA + ++ E Sbjct: 627 EAGAQVEAGAALVRLE 642 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: 1164 Number of extensions: 53 Number of successful extensions: 5 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: 646 Length adjustment: 38 Effective length of query: 628 Effective length of database: 608 Effective search space: 381824 Effective search space used: 381824 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 Apr 10 2024. 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