Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate 201056 SO1894 acetyl-CoA carboxylase, biotin carboxylase, putative (NCBI ptt file)
Query= BRENDA::Q19842 (724 letters) >FitnessBrowser__MR1:201056 Length = 694 Score = 488 bits (1256), Expect = e-142 Identities = 283/690 (41%), Positives = 417/690 (60%), Gaps = 29/690 (4%) Query: 49 FDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKSYL 108 F K+LIANRGEIACR+IKTA+AMG++TVA++SD D N+ HV MADE+ +G + A SYL Sbjct: 12 FTKLLIANRGEIACRIIKTAQAMGVRTVALYSDADKNARHVAMADESFYLGGSAPADSYL 71 Query: 109 RADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHSKK 168 + D I+ + AQA+HPGYGFLSEN FA + E AG F+GP S AI MG K +K Sbjct: 72 KGDLIIAIAKKAQAQAIHPGYGFLSENADFARKCEAAGIVFVGPGSDAIDAMGSKSAAKA 131 Query: 169 IATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQAREGY 228 I TAA+V ++PGY G+ + + IG+P++IKA+ GGGGKGMR+ ++ + + Sbjct: 132 IMTAAQVPLVPGYHGDDQTDATLKAEALKIGFPMLIKAAYGGGGKGMRIVEHEGEIMDAI 191 Query: 229 RLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVIEE 288 +++EAASSFG+D++L+E+++ PRH+E+QV D GNA++L++R+CSIQRR+QKV+EE Sbjct: 192 NSARREAASSFGNDKLLMERYLRQPRHVEVQVFADTFGNAIYLSDRDCSIQRRHQKVVEE 251 Query: 289 APSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEHPITE 348 AP+ + E+R +MGE AV AKA+ Y AGT+EFL+D+ +FYF+EMNTRLQVEHP+TE Sbjct: 252 APAPGLSDELRAQMGEAAVAAAKAIDYVGAGTIEFLLDTDNSFYFMEMNTRLQVEHPVTE 311 Query: 349 CITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLSRYVE 408 +TG D+V+ L V+ G PLP+ Q++V ++G AFE R+YAEDP F LP+ G+L+ E Sbjct: 312 MVTGQDLVKWQLMVASGQPLPLKQDEVRIHGHAFEVRIYAEDPQNEF-LPASGKLNFLRE 370 Query: 409 PKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGVTHNI 468 P+ VR DSGIRE IS +YDP+I KL+ ++R +AL R+ AL++Y I G+ HNI Sbjct: 371 PEQSKYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISGLKHNI 430 Query: 469 PLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALN--ARKLARA 526 L +I + F D +T ++ Y + G++ S E D +AFA+ ARK A Sbjct: 431 EFLANIAEHPAFAKADFSTDFINR-YGDALIGSASS--EADTALAFAALYQVLARKEAAK 487 Query: 527 NQFLNQNKQRST--HVASFSKTYKFVSSLPVKEGERPTEHAVEVEF---VEGSANKA--- 578 Q +N S V+ F S+ + + + V ++F + S N++ Sbjct: 488 AQAINSADPDSPWGQVSGFRLNSVSQHSIALLDDAHELQQLVLLDFGDHYQLSHNRSSQH 547 Query: 579 ----QVRIGGKTVTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKV 634 G + ++SG+ L + E++G H + V + + T+ + + Sbjct: 548 QLSQSAADGQVSKSLSGE--LKQDLLLAEING-HKSKVPVSAQGDDFTLFLPSGSYHFRA 604 Query: 635 LPEQAVKYLQYMKEKAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNS 694 + Q V+ ++K K +PM G + V G V GQ L+VMEAMKM+ + Sbjct: 605 VKTQVVEAESSNEDKLK--------APMNGTVVTHLVDVGAEVKAGQGLLVMEAMKMEYT 656 Query: 695 LHAGKTGRVKAVNVKVGATVDEGEVLVELE 724 + A G V K G V +G VL+ +E Sbjct: 657 IEAPFDGIVTEFYFKAGELVSDGAVLLHVE 686 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: 1100 Number of extensions: 42 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: 694 Length adjustment: 39 Effective length of query: 685 Effective length of database: 655 Effective search space: 448675 Effective search space used: 448675 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: 55 (25.8 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