Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate GFF4239 HP15_4179 methylcrotonyl-CoA carboxylase, alpha subunit
Query= SwissProt::Q5LUF3 (681 letters) >FitnessBrowser__Marino:GFF4239 Length = 664 Score = 497 bits (1279), Expect = e-145 Identities = 291/685 (42%), Positives = 403/685 (58%), Gaps = 50/685 (7%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF+KILIANRGEIACR+I+TA +MGI VA+YS+AD A HV MADEA HIGP P+++SY Sbjct: 1 MFSKILIANRGEIACRIIQTAHRMGIRVVAVYSEADANARHVAMADEAFHIGPAPSSESY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 + +K++ + +GAQA+HPGYGFLSEN+ FAE+ EA ++F+GPP AI AMG K +K Sbjct: 61 LRAEKIIEIAKKSGAQAIHPGYGFLSENTGFAESCEANNIVFIGPPSSAIAAMGSKSAAK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 I ++A V VPGY G + + + + G+P+++KA AGGGGKGMR+ N E + Sbjct: 121 AIMEKAGVPLVPGYHGDDQSVETLRAEAEKCGFPLLLKAVAGGGGKGMRVVNNMGEFDDA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 ++K EA N+FG+ + IE+++TQPRH+EIQV CD G G+YL ER+CS+QRR+QKV+E Sbjct: 181 LAAAKREAQNAFGNPDMLIERYLTQPRHVEIQVFCDQEGKGVYLAERDCSVQRRHQKVLE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAP+P L E TR+AMGE AV A+A+ Y AGTVEF+ D +F+F+EMNTRLQVEHPVT Sbjct: 241 EAPAPGLSEETRKAMGEAAVRAAQAINYVGAGTVEFLYDVDGSFFFMEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 E++TG DLVE ++VA G+ L + Q VK G A+E R+YAEDP + FLP+ G L Sbjct: 301 EMVTGQDLVEWQLKVAWGDALPLEQSQVKTRGHALEARIYAEDPDQDFLPATGNLRYLST 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 P E+ A VR DTGV EG +IS++YDPMIAKL W TR AI Sbjct: 361 PDES-------------------AHVRVDTGVTEGDDISIHYDPMIAKLIVWDETRDQAI 401 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 M AL+ + + G+ N+ FL A+ D F ++TT FI + + P++ L Sbjct: 402 NRMVQALEHYRIAGVKTNIRFLHALADAQPFREAELTTGFI-----DDHRELLFPKSKLD 456 Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMD-------NHERRVGTEWVVTLQGADFPVTIAAD-H 532 A A V E R++R D + R+ +E+ LQ + + + H Sbjct: 457 THKALVLAAGFVLEQRKSREVVSTDPWSPFGRQNSWRMNSEFAQPLQ-----LQVGEEIH 511 Query: 533 DGSTVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVR 592 D + DD + V GD + NL L+ + G RI G + Sbjct: 512 DLKVLERDDRYQVFV------GDSVYNLTARLDDDYLQA--VINGHRISIHGNLHNDQLV 563 Query: 593 TPRQAELARLMPEKLPPDTSKM-----LLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMK 647 + + K +M L PM G IV V +VG +V GQ+L +EAMK Sbjct: 564 LFYEGDTFNCTVYKESYGFEEMAGEGSLAAPMNGAIVAVQAKVGDKVTAGQSLVIMEAMK 623 Query: 648 MENILRAEKKGVVAKINASAGNSLA 672 ME+ ++A GVV +I + G+ ++ Sbjct: 624 MEHAIKAPADGVVTEIFFAEGDQVS 648 Lambda K H 0.317 0.134 0.387 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: 1075 Number of extensions: 51 Number of successful extensions: 3 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: 664 Length adjustment: 39 Effective length of query: 642 Effective length of database: 625 Effective search space: 401250 Effective search space used: 401250 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