Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate YP_004143329.1 Mesci_4168 carbamoyl-phosphate synthase L chain ATP-binding protein
Query= SwissProt::Q5LUF3 (681 letters) >NCBI__GCF_000185905.1:YP_004143329.1 Length = 670 Score = 838 bits (2166), Expect = 0.0 Identities = 430/685 (62%), Positives = 516/685 (75%), Gaps = 21/685 (3%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF KILIANRGEIACRVIKTARKMGI+TVA+YSDAD+ A+HV+MADEAVHIGP PA SY Sbjct: 1 MFTKILIANRGEIACRVIKTARKMGIATVAVYSDADRDAVHVEMADEAVHIGPSPAALSY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 +V +K++AA + TGAQAVHPGYGFLSE + F EALEAEG+IF+GP AI+AMGDKI SK Sbjct: 61 LVPEKIIAACKETGAQAVHPGYGFLSERAAFCEALEAEGIIFIGPKPKAIKAMGDKIESK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 K A A VSTVPG++G+IE+AD A KI+ +IGYPVMIKASAGGGGKGMRIAW++ E R+G Sbjct: 121 KFANAAKVSTVPGWLGVIENADHAEKIAGEIGYPVMIKASAGGGGKGMRIAWSEAEVRDG 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 F +++EA +SFGDDR+FIEKFV PRHIEIQVL D+HGN +YLGERECSIQRRNQKV E Sbjct: 181 FDRARSEAKSSFGDDRLFIEKFVVDPRHIEIQVLADAHGNALYLGERECSIQRRNQKVAE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAPSPFLD ATR+AMGEQ+VALAKAV Y SAGTVEFIVD KNFYFLEMNTRLQVEHPVT Sbjct: 241 EAPSPFLDAATRKAMGEQSVALAKAVDYQSAGTVEFIVDKDKNFYFLEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 ELITG+DLVEQMIRVAAGE L + Q D++L GWA+E+RLYAEDPYR FLPSIGRLTRYRP Sbjct: 301 ELITGIDLVEQMIRVAAGEKLGLKQSDIELNGWAVESRLYAEDPYRNFLPSIGRLTRYRP 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 P E G+ +RNDTGV EG EISM+YDPM+AKLCTWAPTR AI Sbjct: 361 PEE---------------GQFGDVVIRNDTGVTEGSEISMFYDPMLAKLCTWAPTRLEAI 405 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 +AM ALDSF V+GI HN+PFL+A+M H ++ G ++TAFI+EEYP+GF V +P D + Sbjct: 406 DAMSEALDSFVVDGIEHNIPFLAALMQHQRWREGRISTAFISEEYPDGFAPV-VPNDDEK 464 Query: 481 RV-AAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVSF 539 V A+ A A+ + R R+ GR+ H + +WVV + +I + Sbjct: 465 AVLASIATAVELLRRDRLDRLGGRLAPHSGALKRDWVVKIDDDYLSASIIEGMISIPMEV 524 Query: 540 D----DGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTPR 595 D G ++ V SDW PGD + V + +V ++ GFRI +G + PR Sbjct: 525 DLSIAGGKALTVASDWRPGDLVWRGTVGKRKVTAQVRPVANGFRIAWKGMSVTARAMLPR 584 Query: 596 QAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAE 655 AEL RLMPEK+ PDTSK+LLCPMPGL+V + V GQEV+ G+ L +EAMKMEN+LRAE Sbjct: 585 TAELERLMPEKVAPDTSKLLLCPMPGLVVSIAVAEGQEVKAGETLAVVEAMKMENVLRAE 644 Query: 656 KKGVVAKINASAGNSLAVDDVIMEF 680 + VV+K+NA G+SLAVD VIMEF Sbjct: 645 RDLVVSKLNAKPGDSLAVDAVIMEF 669 Lambda K H 0.317 0.134 0.387 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: 1188 Number of extensions: 47 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: 681 Length of database: 670 Length adjustment: 39 Effective length of query: 642 Effective length of database: 631 Effective search space: 405102 Effective search space used: 405102 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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