Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate 8499651 DvMF_0417 pyruvate carboxylase (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >FitnessBrowser__Miya:8499651 Length = 1234 Score = 317 bits (812), Expect = 2e-90 Identities = 190/457 (41%), Positives = 266/457 (58%), Gaps = 7/457 (1%) Query: 9 LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +LVANRG A R+ R+ + VAV +ATD D + + L +YL ID Sbjct: 18 ILVANRGIPARRICRSIRER-FDAVAVMTATDIDKTSPAASAAQELLLLGSDPRAYLDID 76 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128 +IA AK G AIHPG+GF SE+ F +AAGL F+G A A++ +G+K + L + Sbjct: 77 HIIALAKQRGIVAIHPGWGFASEDERFPAKCKAAGLTFIGSTAEAMNLLGNKVQVRKLAK 136 Query: 129 TAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 +P+VPG G A D+ T R + IG PV+LKA GGGG+G+ + +L++A A Sbjct: 137 KLDIPVVPGSEG-AVDIPTARTIIDEIGLPVMLKAEGGGGGRGIFAIHRAEELSDAFMKA 195 Query: 189 QREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 A +SFG+ R+ VEKYL RH+EIQV AD +GN +ERDC++QR HQK++E P+ Sbjct: 196 STMAQASFGNPRLYVEKYLPSVRHIEIQVIADMYGNVFAFDERDCTVQRNHQKLIEITPS 255 Query: 249 P--GLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEA 306 P G++PELR + E + + +GY TVEFL+ A G + +E+NTRLQVEH +TE Sbjct: 256 PWSGITPELRERLKEYSRMLVREVGYHSLCTVEFLVTADGTPYLIEVNTRLQVEHGITEC 315 Query: 307 ITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRESA 366 G+DLV QI VA G L T++ A++VR+ EDP N F P +G ++ Y S Sbjct: 316 RYGIDLVEEQIAVAFGARLRFTEENTTPQHVAMQVRINCEDPQNHFAPNSGLVSRY-VSP 374 Query: 367 AGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNINF 426 GPG R+DS + G E YD LIA+G+ E+ + L E+ IGG+KT + F Sbjct: 375 GGPGVRLDSNMCAGYEFPSNYDSAGSLLIAYGQGWEKVLGIMERCLGEYVIGGIKTTVPF 434 Query: 427 LRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDE 463 ++++ HP F A +LDT FI E L SDL+ E Sbjct: 435 YKQVLKHPKFRAGDLDTNFIANTPE--LMCYSDLAPE 469 Score = 41.6 bits (96), Expect = 2e-07 Identities = 29/105 (27%), Positives = 53/105 (50%), Gaps = 7/105 (6%) Query: 551 DTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEAGAQLVV 610 D+ ++ + ++ + D + +A S+ + AP NG + + V G V+ G +L Sbjct: 1097 DSEFMSCEVQVAKAAVADGKGSEKADPSNPMHVAAPSNGDLWVMYVHPGDVVKQGEELFN 1156 Query: 611 LEAMKMEHSIRAPHAGIIK-----ALYCQEGEM--VSEGSALVEL 648 + MK E ++ AP +G++K A Y + +M V EG +VEL Sbjct: 1157 ISIMKQEKAVLAPVSGMVKRVLKTADYRESKQMMPVREGELIVEL 1201 Lambda K H 0.318 0.134 0.386 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: 1693 Number of extensions: 68 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: 651 Length of database: 1234 Length adjustment: 43 Effective length of query: 608 Effective length of database: 1191 Effective search space: 724128 Effective search space used: 724128 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: 56 (26.2 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