Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate 5210790 Shew_3218 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)
Query= BRENDA::Q19842 (724 letters) >FitnessBrowser__PV4:5210790 Length = 1516 Score = 305 bits (780), Expect = 1e-86 Identities = 178/457 (38%), Positives = 266/457 (58%), Gaps = 13/457 (2%) Query: 50 DKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMA---DEAVCVGEAPTAKS 106 DK+L+ RG A ++I+ A IK V V SD D S+ M D+ VC+G + +S Sbjct: 941 DKVLVHARGCTAVKLIRKAHDNNIKVVLVASDPDMTSVPADMLNENDKLVCIGGNTSDES 1000 Query: 107 YLRADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHS 166 YL A +L+ E A+HPG GFLSE+ +FAA G F+GP+ ++ MG+K ++ Sbjct: 1001 YLNAYSVLKVAEYEQVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNKSNA 1060 Query: 167 KKIATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQARE 226 K + + V ++PG G + + + V V+ +IGYPV++KA GGGGKG++V + Sbjct: 1061 IKTSQSQNVPVVPGSHGILTNAEQAVNVANEIGYPVLLKAVQGGGGKGIQVVQRPEDMIS 1120 Query: 227 GYRLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVI 286 ++ + EAA++FG+ + +EK++ + RHIE+Q+L DK GN L R+CS+QR NQKVI Sbjct: 1121 LFQKTSTEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDKFGNTKVLGLRDCSVQRNNQKVI 1180 Query: 287 EEAPSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRN-FYFLEMNTRLQVEHP 345 EE+ S+ +P E+++++ E L A Y AGTVEF+ + N YF+EMNTRLQVEHP Sbjct: 1181 EESGSTMLPEELKQQVMEYTRALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQVEHP 1240 Query: 346 ITECITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFG-----LPSV 400 +TE +GIDIV ++ G + + Q G+A E RV AE LP Sbjct: 1241 VTEATSGIDIVSAGFDIAAGRSIEDLEPQE--IGYAIEVRVTAEKAALDSNGVLQLLPHP 1298 Query: 401 GRLSRYVEPKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDN-Y 459 G ++ V P+ D + S EG E+S YYD LI +++ G++RE +N++ + L N Sbjct: 1299 GMITECVIPER-DDIEIISIAGEGKEVSPYYDSLIAQIICRGESREDVINKLHDYLANQV 1357 Query: 460 VIRGVTHNIPLLRDIVQEKRFRTGDITTKYLPEVYPE 496 VI+G+ NIPLL I+++ F G T YLP E Sbjct: 1358 VIKGIATNIPLLTRILKDGTFNEGVYDTNYLPRFMAE 1394 Score = 27.7 bits (60), Expect = 0.005 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 2/47 (4%) Query: 660 SPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNSLHAGKTGRVKAV 706 SP PG V K GD+V+ Q L + EAMKM + + R AV Sbjct: 1439 SPAPGEADFV--KEGDIVTVDQTLALTEAMKMFSQVTLAGFNRQGAV 1483 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: 2218 Number of extensions: 93 Number of successful extensions: 5 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: 724 Length of database: 1516 Length adjustment: 45 Effective length of query: 679 Effective length of database: 1471 Effective search space: 998809 Effective search space used: 998809 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: 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