Align propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized)
to candidate Pf6N2E2_2194 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= BRENDA::P05165 (728 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2194 Length = 649 Score = 498 bits (1281), Expect = e-145 Identities = 284/668 (42%), Positives = 402/668 (60%), Gaps = 33/668 (4%) Query: 66 ILVANRGEIACRVIRTCKKMGIKTVAIHSDVDASSVHVKMADEAVCVGPAPTSKSYLNMD 125 +LVANRGEIACRV+RT K MG+ TVA+HS D + H + AD V +G + + SYL +D Sbjct: 9 LLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 Query: 126 AIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAEDVVFIGPDTHAIQAMGDKIESKLLAK 185 ++ A K + AQA+HPGYGFLSEN FAR + ++F+GP AI AMG K +K L + Sbjct: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALME 128 Query: 186 KAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRLS 245 A V +PG+ G +D E A IGYPV++KA+AGGGGKGM++ D + + + Sbjct: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 Query: 246 SQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEEAPS 305 +EA SSFGD R+L+EK++ PRH+EIQV D+HGN L+LNER+CSIQRR+QKVVEEAP+ Sbjct: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 Query: 306 IFLDAETRRAMGEQAVALARAVKYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECIT 365 L A+ R+AMGE AV A+A+ Y AGTVEFL+D++ F+F+EMNTRLQVEHPVTE IT Sbjct: 249 PGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308 Query: 366 GLDLVQEMIRVAKGYPLRHKQADIRINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPLH 425 GLDLV IRVA+G PL QA + + G A+E R+YAEDP F LP+ GRL+ Y+E Sbjct: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDF-LPATGRLALYRESAK 367 Query: 426 LPGVRVDSGIQPGSDISIYYDPMISKLITYGSDRTEALKRMADALDNYVIRGVTHNIALL 485 PG RVDSG++ G +IS +YDPM+ KLI +G +R +A R+ LD + I G+ NI L Sbjct: 368 GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTNIGFL 427 Query: 486 REVIINSRFVKGDISTKFLSDVYPDGFKGHMLTKSEKNQLLAIASSLFVAFQLRAQHFQE 545 R ++ + F ++ T F+ + QLL L AF L A Sbjct: 428 RRIVAHPAFAAAELDTGFI--------------PRYQAQLLPEPGELDDAFWLAAAQGFA 473 Query: 546 NSRMPVIKPDIAN--WELSVKLH---DKVHTVVASNNGSVFSVEVDGSKLNVTSTWNLAS 600 S P I+ D A W + + + T+ S G ++ +D + L Sbjct: 474 LSLAPHIRGDDAGSPWASTTGMRLGLSRETTLHLSCEGQDRALTLDVT----AHCAELKG 529 Query: 601 PLLSVSVDGTQRTVQCLSREAGGNMSIQFLGTVYKVNILTRLAAELNKFMLEKVTEDTSS 660 L++ G +R+ + + + G ++ + + G ++++++ LAA + + Sbjct: 530 ERLTIEHHGVRRSHRAIRQ--GDSLYLHWAGDLHRIDLYDPLAA-------AEASHSHQG 580 Query: 661 VLRSPMPGVVVAVSVKPGDAVAEGQEICVIEAMKMQNSMTAGKTGTVKSVHCQAGDTVGE 720 L +PM G +V V V G V G ++ V+EAMKM++S+ A K G +K+++CQ G+ V E Sbjct: 581 GLAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSE 640 Query: 721 GDLLVELE 728 G LV E Sbjct: 641 GSALVAFE 648 Lambda K H 0.318 0.134 0.385 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: 1039 Number of extensions: 35 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: 728 Length of database: 649 Length adjustment: 39 Effective length of query: 689 Effective length of database: 610 Effective search space: 420290 Effective search space used: 420290 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