Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate PfGW456L13_2284 Geranyl-CoA carboxylase biotin-containing subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2284 Length = 653 Score = 581 bits (1498), Expect = e-170 Identities = 327/661 (49%), Positives = 417/661 (63%), Gaps = 25/661 (3%) Query: 4 PALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADS 63 P L +L+ANRGEIACR+ RTA+A+G TVAV S D DA H R AD V++G + S Sbjct: 2 PGLKKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVRIADEAVNIGPAPVQQS 61 Query: 64 YLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAA 123 YL I ++ AA+ +GA AIHPGYGFLSENAGFA A +AG+ F+GP AI+ MGSK + Sbjct: 62 YLNIQAILDAARRTGADAIHPGYGFLSENAGFALACRDAGITFIGPSPEAIELMGSKRLS 121 Query: 124 KALMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183 K M AGVP + GY G QD T AERIGYP+++KA+AGGGG+GM++V D S L E Sbjct: 122 KIAMIEAGVPCINGYQGAGQDDATLGREAERIGYPLMIKASAGGGGRGMRLVHDASDLLE 181 Query: 184 ALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243 + +A+ EA + FG +++E+ L++PRHVE+Q+F D+HGN +YL ERDCS+QRRHQKV+ Sbjct: 182 QIRTARSEALNGFGSGELILEQALVEPRHVEVQLFGDRHGNLIYLGERDCSVQRRHQKVI 241 Query: 244 EEAPAPGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPV 303 EEAP P +TA+LRQAMGEAA++A +A+ YVGAGTVEFLLDARG+F+F+EMNTRLQVEHPV Sbjct: 242 EEAPCPVMTAELRQAMGEAALKAGRAVKYVGAGTVEFLLDARGQFYFLEMNTRLQVEHPV 301 Query: 304 TEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLALYR 363 TE ITGLDLVAWQ+ +A+G+PLP+ Q QV L GHA+EVRLYAEDP FLP TGR+ + Sbjct: 302 TELITGLDLVAWQLSIAEGQPLPLRQEQVQLTGHAMEVRLYAEDPAQGFLPQTGRVVAW- 360 Query: 364 ESAKGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTN 423 E A G R+D G+ EG ISPFYDPMLGKLIA G RE+AR +LL + + + GLK+N Sbjct: 361 EPALQDGVRIDHGLIEGQVISPFYDPMLGKLIAHGATREEARRKLLRAVQDSVLLGLKSN 420 Query: 424 IGFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPGELDDAFWLAAAQGFALSLAPHIRGD 483 L ++ HP FA+ + TGFI ++ E A LA A A Sbjct: 421 QRLLASLLEHPQFASGDFSTGFIAQHFTDHTCLHPETPGAHHLAIAAALFYQAA------ 474 Query: 484 DAGSPWASTTGMRLGLSRETTLHLSCEGQD----------RALTLDVTAHCAELK----- 528 A + A G R S + E QD L + V ELK Sbjct: 475 -AQAHLAPLGGWRNNASVPLHYRIGLEDQDWPVALQAIPGEPLRIQVAERSLELKIIHSD 533 Query: 529 GERLTIEHHGVRRSHRAIRQGDSLYLHW-AGDLHRIDLYDPLAAAEASHSHQGGLAAPMN 587 G T+E GVR+ H + L L G L +D +AS S G L APM+ Sbjct: 534 GRWATLEIEGVRQRHAYRLEAGRLRLFTRPGSLQFVDRTQVQVTGQASVS-SGTLKAPMD 592 Query: 588 GSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSALVAF 647 G+IV VLV+ G V G LVVLEAMKMEH +++ GV+K L + G+ V L+ Sbjct: 593 GAIVDVLVNEGSQVTKGQLLVVLEAMKMEHPLKSGIDGVLKRLQVKVGDQVKNRQILLEV 652 Query: 648 E 648 E Sbjct: 653 E 653 Lambda K H 0.319 0.134 0.389 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: 1081 Number of extensions: 46 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: 649 Length of database: 653 Length adjustment: 38 Effective length of query: 611 Effective length of database: 615 Effective search space: 375765 Effective search space used: 375765 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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