Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate BPHYT_RS23275 BPHYT_RS23275 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__BFirm:BPHYT_RS23275 Length = 692 Score = 494 bits (1272), Expect = e-144 Identities = 302/700 (43%), Positives = 400/700 (57%), Gaps = 49/700 (7%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 MF KILIANRGEIACRV T +++GI +VA+YSDAD NA HV DEAVHIG S A +SY Sbjct: 1 MFNKILIANRGEIACRVAATCKRLGIASVAVYSDADANAKHVAACDEAVHIGGSTAAESY 60 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + ++++++A R TGA+AVHPGYGFLSEN+ FA A E G+ FIGPP AI AMG K +K Sbjct: 61 LRVERIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAK 120 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 + A V VPGY G DA + + IGYPV++KASAGGGGKGMR+ + Sbjct: 121 ALMHTAAVPLVPGYHGDDQDAQLLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFEAA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 S K EAA+SFG+DR+ IEK++T+PRH+E+QV AD HG +YL +R+CS+QRR+QKV+E Sbjct: 181 LASCKREAASSFGNDRVLIEKYLTRPRHVEVQVFADRHGGAVYLFDRDCSVQRRHQKVLE 240 Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300 EAP+P L ++ MG+ + A A+AV Y AGTVEFI+ G +FYF+EMNTRLQVEHPVT Sbjct: 241 EAPAPGLAAEIKREMGDAAVAAARAVNYVGAGTVEFIMTGTGDFYFMEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360 E++TG DLVE +RVAAGE LP+TQ+ + + G AIE R+YAE P R FLPS G L R Sbjct: 301 EMVTGQDLVEWQLRVAAGEALPLTQEQLKIDGHAIEARIYAEHPARGFLPSTGTLKHLRM 360 Query: 361 PVEVAAGPLEANGKWHGDAPSGPTA-VRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAA 419 P V A G SG A VR D+GV EG I+ +YDPMIAKL G R A Sbjct: 361 PEGVEFTLDAAGSGAAGLGESGRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGATREEA 420 Query: 420 IEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGF--------EG 471 + M AL EV G N+ F+ +++ F G++ T I+ + F E Sbjct: 421 LARMSRALHACEVVGPHTNVEFLQSIVASEPFATGDLDTGLIERHHDALFAPRKKPFKEA 480 Query: 472 VTLGAADLTR----LAAAAAAMFRVAEIR----RTRISGTLDNHERMVGTDWVVTAQDAR 523 + L A L + A A+ ++ R T+ G D G + ++ Sbjct: 481 LALACAALLKREGGTAHGASPWDALSHWRLNGGYTQTLGWRDLESGSAGN--AGSDSEST 538 Query: 524 FDVTIDADPGGSTVR---------FADGTAHRVTSRWTPGDSLAT--VEIDGAPMVLKVD 572 F VT D G T+ ++DG+ R T GD+ AT V +DG + Sbjct: 539 FTVTFARDGGTQTLEHDGVREDFSWSDGSGLH-EYRATIGDARATGRVFVDGDTFHV--- 594 Query: 573 KITSGFRMRFRGADVKVHVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGD 632 G + F ++ H E L PMPG V+ + VE G Sbjct: 595 -FCLGEALSFEWQNLLAHAADAEGGE--------------GRLTAPMPGKVIAVLVEPGT 639 Query: 633 EVQEGQALCTVEAMKMENILRAEKTATVTKINAGAGDSLA 672 V++G L +EAMKME+ + A TV+++ GD +A Sbjct: 640 VVEKGTPLIVMEAMKMEHTIGAPAAGTVSEVLYSVGDQVA 679 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: 1211 Number of extensions: 62 Number of successful extensions: 4 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: 681 Length of database: 692 Length adjustment: 39 Effective length of query: 642 Effective length of database: 653 Effective search space: 419226 Effective search space used: 419226 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