Align Propionyl-CoA carboxylase alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate 200026 SO0840 acetyl-CoA carboxylase multifunctional enzyme accADC, carboxyl transferase subunit alpha/carboxyl transferase subunit beta/biotin carboxylase (NCBI ptt file)
Query= SwissProt::P0DTA4 (730 letters) >FitnessBrowser__MR1:200026 Length = 1517 Score = 310 bits (795), Expect = 3e-88 Identities = 174/453 (38%), Positives = 273/453 (60%), Gaps = 12/453 (2%) Query: 61 KTFDKILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTM---ADEAVCVGPAPT 117 K +K+L+ RG A ++I+ I V V SD D ++V M +D+ VC+G + Sbjct: 938 KPINKVLVHARGCTAVKLIRKAHDNNINVVLVASDPDMTAVPADMLKESDKLVCLGGNTS 997 Query: 118 SKSYLNMDAIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDK 177 +SYLN ++++ + A+HPG GFLSE+ +FA GV F+GP H++ MG+K Sbjct: 998 DESYLNAYSVLKVAEYEQVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNK 1057 Query: 178 IESKLLAKKAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEE 237 + ++ V +PG G++ +A++AV +A EIGYPV++KA GGGGKG+++ E+ Sbjct: 1058 SNAIKTSQAQNVPVVPGSHGILTNAEQAVNVASEIGYPVLLKAVQGGGGKGIQVVKRPED 1117 Query: 238 TRDGFRFSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQ 297 F+ ++ EAA++FG+ L +EK++ + RHIE+Q+L DK G+A L R+CS+QR NQ Sbjct: 1118 MIGLFQKTATEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDKFGHAKVLGLRDCSVQRNNQ 1177 Query: 298 KVVEEAPSIFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKKN-FYFLEMNTRLQV 356 KVVEE+ S L E ++ + AL A +Y AGTVEF+ + N YF+EMNTRLQV Sbjct: 1178 KVVEESGSTMLPDELKKQVLAYTRALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQV 1237 Query: 357 EHPVTECITGLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAED-PYKSFG----L 411 EHPVTE +G+D+V +A G + H + G+A+E RV AE S G + Sbjct: 1238 EHPVTEATSGIDIVSAQFDIAAGRSIEHLEP--KEIGYAMEVRVTAEKAALDSHGVLQLI 1295 Query: 412 PSIGRLSQYQEPIHLPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALD 471 P+ G++++ P H P V + S PG ++S YYD +I+++I G NR + + ++ LD Sbjct: 1296 PNPGKITECVFPDH-PDVEIISIAAPGKEVSPYYDSLIAQVIMRGENREDVIAKLHAYLD 1354 Query: 472 NYVIRGVTHNIALLREVIINSRFVEGDINTKFL 504 + V++G+ NI LL+ ++ + F EG +T +L Sbjct: 1355 SVVLKGIATNIPLLKLILSDGTFKEGVYDTNYL 1387 Score = 28.9 bits (63), Expect = 0.002 Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 15/87 (17%) Query: 653 LEKAAEDTSSILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAG-------- 704 L+ A+ SP PG VK GD+V Q + + EAMKM + + Sbjct: 1425 LKVLAQGAGIFYTSPAPGE--PDFVKEGDIVTAEQTLALTEAMKMFSQVNLAGFNRQGAV 1482 Query: 705 -----KTGKVKSVHCKAGDTVGEGDLL 726 K +++ + G V +GDLL Sbjct: 1483 LYPEDKKYRIERILNSNGQQVSQGDLL 1509 Lambda K H 0.318 0.134 0.385 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: 2148 Number of extensions: 82 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 730 Length of database: 1517 Length adjustment: 45 Effective length of query: 685 Effective length of database: 1472 Effective search space: 1008320 Effective search space used: 1008320 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 (21.7 bits) S2: 58 (26.9 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