Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_088755445.1 CEJ45_RS12575 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Dino:3607308 (681 letters) >NCBI__GCF_002213425.1:WP_088755445.1 Length = 671 Score = 529 bits (1362), Expect = e-154 Identities = 312/696 (44%), Positives = 408/696 (58%), Gaps = 42/696 (6%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 MF KILIANRGEIACRV TAR++GI TVA+YSDAD A HV DE+VH+GP+PA +SY Sbjct: 1 MFTKILIANRGEIACRVAATARRLGIATVAVYSDADAQAKHVAACDESVHLGPAPAKESY 60 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + DK++ A TGA+A+HPGYGFLSEN FA+A G+ FIGPPA+AIEAMG K +K Sbjct: 61 LCADKIIAAALATGAQAIHPGYGFLSENAGFAQACADAGLVFIGPPASAIEAMGSKSAAK 120 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 + ++A V VPGY G ++D + IGYPV++KASAGGGGKGMR+ + Sbjct: 121 ALMEKAAVPLVPGYHGQRQESDFLRTEADRIGYPVLLKASAGGGGKGMRVVERSEDFEVA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 S K EA +SFGDDR+ +EK++T+PRHIEIQV AD HG+C+YL ER+CS+QRR+QKV+E Sbjct: 181 LASCKREAISSFGDDRVLVEKYLTRPRHIEIQVFADGHGHCVYLFERDCSVQRRHQKVLE 240 Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300 EAP+P + R AMGE + A A+AVGY AGTVEFI + D FYF+EMNTRLQVEHPVT Sbjct: 241 EAPAPGMSCGRRAAMGEAAVAAARAVGYVGAGTVEFIANQDGTFYFMEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYR- 359 E+ITG+DLVE +RVA+GE LP+ Q+ + + G AIE R+YAE+P + FLP+IG LTR R Sbjct: 301 EMITGLDLVEWQLRVASGEPLPLKQEQLRIQGHAIEARIYAENPEKGFLPAIGTLTRMRS 360 Query: 360 -PPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPA 418 P VE A L A G + P AVR D GV EG IS +YDPMIAKL WG DR A Sbjct: 361 APAVEFA---LAAPG------ATQPAAVRIDAGVREGDAISPFYDPMIAKLIVWGADRDA 411 Query: 419 AIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAAD 478 A+ M AL ++V G+ N+ F+ ++ F ++ T I+ F AD Sbjct: 412 ALRNMARALAQYQVVGLATNIGFLQRLIAGQAFATADLDTGLIERHRDTLFPAPVAPTAD 471 Query: 479 LTRLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPGGSTVR 538 LA AA R R + D + G W + + R + + D G S VR Sbjct: 472 TLALATAALLQ------REQRNQDSRDPWAQTSG--WRLNTRLQRC-LNFEHDSGNSEVR 522 Query: 539 F------------ADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGAD 586 G H + DS+ + +DG + V G + F G Sbjct: 523 IDYAGDGRQWQLQIGGNTHTLALHAANTDSV-RISLDGRTLQADVAWEGEGLHL-FDG-- 578 Query: 587 VKVHVRTPRQAELNDLMPEKLPPDT-SKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEA 645 R+ L D M + L PMPG +V + V+ G V +G L +EA Sbjct: 579 -----RSQHSLRLPDPMAHAGHAEAEGGRLTAPMPGKIVALLVDQGASVTQGTPLLIMEA 633 Query: 646 MKMENILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681 MKME+ + A TV + GD +A +++F+ Sbjct: 634 MKMEHTIAAPSAGTVEALRYAVGDQVAEGAQLLDFK 669 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: 1161 Number of extensions: 57 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 681 Length of database: 671 Length adjustment: 39 Effective length of query: 642 Effective length of database: 632 Effective search space: 405744 Effective search space used: 405744 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