Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate 7024491 Shewana3_1669 3-methylcrotonoyl-CoA carboxylase, alpha subunit (RefSeq)
Query= BRENDA::Q19842 (724 letters) >FitnessBrowser__ANA3:7024491 Length = 674 Score = 492 bits (1266), Expect = e-143 Identities = 280/678 (41%), Positives = 412/678 (60%), Gaps = 19/678 (2%) Query: 51 KILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKSYLRA 110 K+LIANRGEIACR+IKTA+AMG++TVA++SD D N+ HV MADE+ +G + A SYL+ Sbjct: 4 KLLIANRGEIACRIIKTAQAMGVRTVALYSDADKNARHVAMADESFYLGGSAPADSYLKG 63 Query: 111 DRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHSKKIA 170 D I++ + AQA+HPGYGFLSEN FA + E AG F+GP S AI MG K +K I Sbjct: 64 DLIIEIAKKAQAQAIHPGYGFLSENADFARKCEAAGIVFVGPGSDAIDAMGSKSAAKAIM 123 Query: 171 TAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQAREGYRL 230 TAA+V ++PGY G+ + + IG+P++IKA+ GGGGKGMR+ ++ + + Sbjct: 124 TAAQVPLVPGYHGDDQTDATLKAEALKIGFPMLIKAAYGGGGKGMRIVEHEGEIMDAINS 183 Query: 231 SKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVIEEAP 290 +++EAASSFG+D++L+E+++ PRH+E+QV D GNA++L++R+CSIQRR+QKV+EEAP Sbjct: 184 ARREAASSFGNDKLLMERYLRQPRHVEVQVFADTFGNAIYLSDRDCSIQRRHQKVVEEAP 243 Query: 291 SSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEHPITECI 350 + + E+R +MGE AV AKA+ Y AGTVEFL+D+ +FYF+EMNTRLQVEHP+TE + Sbjct: 244 APGLSDELRTQMGEAAVAAAKAIDYVGAGTVEFLLDTDNSFYFMEMNTRLQVEHPVTEMV 303 Query: 351 TGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLSRYVEPK 410 TG D+V+ L V+ G PLP+ Q++V ++G AFE R+YAEDP F LP+ G+L+ EP+ Sbjct: 304 TGQDLVKWQLMVASGQPLPLKQDEVRIHGHAFEVRIYAEDPQNEF-LPASGKLNFLREPE 362 Query: 411 HVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGVTHNIPL 470 VR DSGIRE IS +YDP+I KL+ ++R +AL R+ AL++Y I G+ HNI Sbjct: 363 QSKYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISGLKHNIEF 422 Query: 471 LRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALN--ARKLARANQ 528 L +I + F D +T ++ G S + E D +AFA+ ARK A Q Sbjct: 423 LANIAEHPAFAKADFSTDFINRY---GDALISSASSETDTALAFAALYQVLARKEAAKAQ 479 Query: 529 FLNQNKQRST--HVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSANKAQVRIGGKT 586 +N S V+ F S+ + + + V ++F + G + Sbjct: 480 AINSADPYSPWGQVSGFRLNSVSQHSIALLDDAHELQQLVLLDFGDHYQLSQPTADGQVS 539 Query: 587 VTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLPEQAVKYLQYM 646 ++SG+ L + E++G H + V + + T+ + + + Q V+ Sbjct: 540 KSLSGE--LKQDLLLAEING-HKSKVPVSAQGDDFTLFLPSGSYHFRAVKTQVVEAESSN 596 Query: 647 KEKAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNSLHAGKTGRVKAV 706 ++K K +PM G + V+ G V+ GQ L+VMEAMKM+ ++ A G V Sbjct: 597 EDKLK--------APMNGTVVTHLVEVGAEVNAGQGLLVMEAMKMEYTIEAPFDGIVTEF 648 Query: 707 NVKVGATVDEGEVLVELE 724 K G V +G VL+ +E Sbjct: 649 YFKAGELVSDGAVLLHVE 666 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: 1091 Number of extensions: 44 Number of successful extensions: 3 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: 724 Length of database: 674 Length adjustment: 39 Effective length of query: 685 Effective length of database: 635 Effective search space: 434975 Effective search space used: 434975 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