Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate PP_4067 PP_4067 methylcrotonyl-CoA carboxylase biotin-containing subunit alpha
Query= BRENDA::Q19842 (724 letters) >FitnessBrowser__Putida:PP_4067 Length = 650 Score = 501 bits (1289), Expect = e-146 Identities = 291/679 (42%), Positives = 407/679 (59%), Gaps = 32/679 (4%) Query: 45 NEPKFDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTA 104 + P +L+ANRGEIACRV++TA+AMG+ TVAVHS D ++ H + AD V +G A Sbjct: 2 SRPALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGTKAA 61 Query: 105 KSYLRADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKI 164 +SYL D++L A + +GAQA+HPGYGFLSEN FA +E+AG F+GP + AI MG K Sbjct: 62 ESYLLVDKLLAAAKASGAQAIHPGYGFLSENAGFARAIEQAGLIFLGPPASAIDAMGSKS 121 Query: 165 HSKKIATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQA 224 +K + AA V ++PGY GE D D + IGYPV++KASAGGGGKGM+V + Q Sbjct: 122 AAKALMEAAGVPLVPGYHGEAQDLDTFRAAAERIGYPVLLKASAGGGGKGMKVVEEESQL 181 Query: 225 REGYRLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQK 284 + +++EA SSFGD RMLVEK++ PRH+E+QV D+HGN L+LNER+CSIQRR+QK Sbjct: 182 ADALASAQREAQSSFGDARMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQK 241 Query: 285 VIEEAPSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEH 344 V+EEAP+ + PE+RR MGE AV+ A+A+GY AGTVEFL+D++ F+F+EMNTRLQVEH Sbjct: 242 VVEEAPAPGLSPELRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEH 301 Query: 345 PITECITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLS 404 P+TE ITG+D+V +RV+ G LPITQEQVPL G A E R+YAEDP F LP+ G+L+ Sbjct: 302 PVTEAITGLDLVAWQIRVACGEALPITQEQVPLIGHAIEVRLYAEDPANDF-LPATGKLA 360 Query: 405 RYVEPKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGV 464 Y E +G R DSG+ EG +S +YDP++ KL+ G++REQA R+ LD + I G+ Sbjct: 361 LYRESAPGEGRRVDSGVSEGDVVSPFYDPMLGKLIAWGEDREQARLRLLAMLDEFAIGGL 420 Query: 465 THNIPLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALNARKLA 524 NI LR I+ F ++ T ++ P+ QDV++ AL A Sbjct: 421 KTNIAFLRRILAHPAFAAAELDTGFI--------------PRHQDVLLPAPRALPAAFWE 466 Query: 525 RANQFLNQNKQRSTHVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSANKAQVRIGG 584 A + Q + + + L + R + H V + A + R Sbjct: 467 AAAEAWLQGQAGHQREDDRHSPWSGSNGLRLGLPARSSLHLVSAGQDQAVALE---RSAA 523 Query: 585 KTVTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLPEQAVKYLQ 644 T + G+ L H N + +H+ +R G + + ++G ++ A Sbjct: 524 STWQLQGE-QLVHDQNGVR--RQHLAI----RRGGTLYLHWEGEMHAIEAFDPIA----- 571 Query: 645 YMKEKAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNSLHAGKTGRVK 704 + +A + +PM G+I V V+PG +V G L+V+EAMKM++S+ A G VK Sbjct: 572 --EAEASHSHQGGLGAPMNGSIVRVLVEPGQVVEAGTALLVLEAMKMEHSIRAPHAGTVK 629 Query: 705 AVNVKVGATVDEGEVLVEL 723 A+ G V EG VLVEL Sbjct: 630 ALFCLEGDMVSEGTVLVEL 648 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: 1086 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: 650 Length adjustment: 39 Effective length of query: 685 Effective length of database: 611 Effective search space: 418535 Effective search space used: 418535 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