Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_097030694.1 CRO07_RS10735 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Dino:3607308 (681 letters) >NCBI__GCF_900207575.1:WP_097030694.1 Length = 646 Score = 469 bits (1207), Expect = e-136 Identities = 283/687 (41%), Positives = 389/687 (56%), Gaps = 51/687 (7%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 MF+KILIANRGEIACRVI TAR++GI TVA++SDAD ALHV +AD++ HIG + SY Sbjct: 1 MFRKILIANRGEIACRVIATARRLGISTVAVFSDADAAALHVALADDSRHIGGAQPADSY 60 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + D+++ A TGAEA+HPGYGFLSEN F + + G+ FIGP A+AI AMG K +K Sbjct: 61 LRADRIIQAALATGAEAIHPGYGFLSENPDFVDQVTAAGLTFIGPSADAIRAMGLKDAAK 120 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 + ++A V VPGY G + D ++ EIGYPV+IKA AGGGGKGMR A+ + Sbjct: 121 ALMEKAGVPVVPGYHGEDQEPDHLAVMAAEIGYPVLIKAVAGGGGKGMRRVDRAADFADA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 S++ EA +FG+D + IEK++ QPRHIEIQ+ D + ++L ER+CS+QRR+QKV+E Sbjct: 181 LASARAEARTAFGNDAVLIEKYIDQPRHIEIQIFGD-GTDAVHLHERDCSLQRRHQKVIE 239 Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGD-----RNFYFLEMNTRLQV 295 EAP+P + R AMGE + A+A+GY AGT EFIVDG F+F+EMNTRLQV Sbjct: 240 EAPAPGMTPEMRAAMGEAAVRAARAIGYRGAGTCEFIVDGSDGLRPDRFWFMEMNTRLQV 299 Query: 296 EHPVTELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRL 355 EHPVTE +TG+DLVE +R+A+GE LP+TQ + L G A E RLYAED FLP+ GRL Sbjct: 300 EHPVTEAVTGIDLVEWQLRIASGEPLPLTQAQIPLIGHAFEARLYAEDVPAGFLPATGRL 359 Query: 356 TRYRPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPD 415 R A+G +R DTGV G IS +YDPMIAK+ GP Sbjct: 360 DHLR----------FADG------------IRADTGVRSGDRISPWYDPMIAKIVAHGPS 397 Query: 416 RPAAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLG 475 R AA+ + AL+ EV G NL F++ + HP F G + T I + + Sbjct: 398 RAAALNRLARALEDTEVAGTVTNLAFLSRLARHPGFAAGRVDTGLIARDIASLTDPAPVT 457 Query: 476 AADLTRLAAAAAAMFRVAEIRRTRISGTLDNHERM-VGTDWVVTAQDARFDVTIDADPGG 534 A A A ++ + L H R+ +G D + A +T+D PG Sbjct: 458 PAITAAALLTAELGTAAAPLQGFTLWSPLRRHARLRLGADEIAAA------ITLDG-PGR 510 Query: 535 STVRFADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVRTP 594 + V A T +++R P E++G +V + + R V+ + P Sbjct: 511 ARVELAGAT---LSARLKP----EGWEVEGTHPG-RVLCLPDAVHVFARSGTVRFTIPDP 562 Query: 595 RQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRA 654 +D T + L PMPGLV ++ V G+ V++G L +EAMKME++L A Sbjct: 563 FDRGTDD-------GATGGLTLSPMPGLVREVAVRPGERVEKGDRLAVIEAMKMEHVLTA 615 Query: 655 EKTATVTKINAGAGDSLAVDDVIMEFE 681 + TV ++ G + ++ E Sbjct: 616 ARDGTVAEVLVEPGAQVEAGAALVRLE 642 Lambda K H 0.318 0.134 0.392 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: 1184 Number of extensions: 53 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 681 Length of database: 646 Length adjustment: 38 Effective length of query: 643 Effective length of database: 608 Effective search space: 390944 Effective search space used: 390944 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