Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate Pf1N1B4_3984 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= BRENDA::Q19842 (724 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3984 Length = 651 Score = 494 bits (1272), Expect = e-144 Identities = 291/691 (42%), Positives = 411/691 (59%), Gaps = 58/691 (8%) Query: 47 PKFDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKS 106 P +L+ANRGEIACRV++TA+A+G+ TVAVHS D ++ H + AD V +G + A S Sbjct: 4 PVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADS 63 Query: 107 YLRADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHS 166 YL+ D+++ A + +GAQA+HPGYGFLSEN FA +E AG F+GP + AI MG K + Sbjct: 64 YLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAA 123 Query: 167 KKIATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQARE 226 K + A V ++PGY GE D + IGYPV++KA+AGGGGKGM+V + Q E Sbjct: 124 KALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183 Query: 227 GYRLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVI 286 +++EA SSFGD RMLVEK++ PRH+E+QV D+HGN L+LNER+CSIQRR+QKV+ Sbjct: 184 ALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243 Query: 287 EEAPSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEHPI 346 EEAP+ + PE+RR MGE AV+ A+A+GY AGTVEFL+D++ F+F+EMNTRLQVEHP+ Sbjct: 244 EEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPV 303 Query: 347 TECITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLSRY 406 TE ITG+D+V +RV+ G LP+TQ+QVPL G A E R+YAEDP F LP+ GRL+ Y Sbjct: 304 TEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDF-LPATGRLALY 362 Query: 407 VEPKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGVTH 466 E G R DSG+ EG EIS +YDP++ KL+ G++REQA R+ LD + I G+ Sbjct: 363 RESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKT 422 Query: 467 NIPLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALNARKLARA 526 NI LR I+ F ++ T ++P Y E L P D+ F A A Sbjct: 423 NINFLRRIIGHPAFAAAELDTGFIPR-YQE-----QLLPAPSDLSDEFWQA--------A 468 Query: 527 NQFLNQNKQRSTHVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSANKAQVRIGGKT 586 Q Q++ +T S + + PTE + + E + Sbjct: 469 AQAFAQSQSSTTRADDLSSPWGIGNGF---RAGLPTEITLHLSCEEQD----------RA 515 Query: 587 VTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLPEQAVKYLQYM 646 +T+ GD + ++ ++ GE++ T+ + G + + + YLQ+ Sbjct: 516 LTL-GDAD----AHTAQLKGEYLLTE------------HNGLRRQHRAIRRGDTLYLQWD 558 Query: 647 KEKAKVD----LSTV---------VLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQN 693 E +++ +S V + +PM G+I V V+ G V G +LVV+EAMKM++ Sbjct: 559 GELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEAGAQLVVLEAMKMEH 618 Query: 694 SLHAGKTGRVKAVNVKVGATVDEGEVLVELE 724 S+ A G +KA+ + G V EG LVELE Sbjct: 619 SIRAPHAGIIKALYCQEGEMVSEGSALVELE 649 Lambda K H 0.316 0.133 0.378 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: 1088 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 724 Length of database: 651 Length adjustment: 39 Effective length of query: 685 Effective length of database: 612 Effective search space: 419220 Effective search space used: 419220 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 (21.6 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