Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate PP_4065 PP_4065 methylcrotonyl-CoA carboxylase biotin-containing subunit beta
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__Putida:PP_4065 Length = 535 Score = 720 bits (1859), Expect = 0.0 Identities = 354/535 (66%), Positives = 417/535 (77%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M+ +H+ I P S +F N A LR LAQ+ QGGG + + RH RGKL R+RI Sbjct: 1 MATLHTQINPRSAEFAVNSAAMLEQVQALRGLLAQVAQGGGPKAQERHTSRGKLLPRERI 60 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120 D L+DP S FLEIG LAA+ VY E+VPAAG++ GIGRV G MI+ANDATVKGG+Y+PL Sbjct: 61 DRLLDPGSPFLEIGQLAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120 Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180 TVKKHLRAQ IA +NRLPCIYLVDSGGA LP Q EVFPDR+HFGRIF+NQA MSA+GIPQ Sbjct: 121 TVKKHLRAQTIALQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180 Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240 IA VMGSCTAGGAYVPAM+DE ++V+ TIFL GPPLVKAATGE V+AE+LGGADVH R Sbjct: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCR 240 Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300 SGVAD++A++D ALAI R VA+L + + P P Y E+YG++P D +Q Sbjct: 241 TSGVADHYADNDEHALAIARRSVANLNWHKLGKLQRLAPVAPLYAADELYGVVPADAKQP 300 Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360 +DVREVIAR+VDGS EFK +GTTLVCGFAH+ G+PV ILANNGILF+E+A KGAHFI Sbjct: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPVAILANNGILFAEAAQKGAHFI 360 Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420 EL C R IPL+FLQNITGFMVGK+YE GGIAK GAKLVTAV+CA VPKFTVIIGGSFGAG Sbjct: 361 ELACQRGIPLLFLQNITGFMVGKKYEEGGIAKHGAKLVTAVACAQVPKFTVIIGGSFGAG 420 Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480 NYGMCGRAY PR LWMWPNARI VMG QAA VL ++R+ GQ + E++ R P Sbjct: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLAQVKREQSERSGQPFSAEDEARLKQP 480 Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 IL +YE++GHPYY+SARLWDDGVIDP +TR VL L L+AA AP++ +RFG+FRM Sbjct: 481 ILDQYERQGHPYYSSARLWDDGVIDPAQTRDVLGLALSAALNAPIEQSRFGIFRM 535 Lambda K H 0.322 0.139 0.423 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: 954 Number of extensions: 32 Number of successful extensions: 2 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: 535 Length of database: 535 Length adjustment: 35 Effective length of query: 500 Effective length of database: 500 Effective search space: 250000 Effective search space used: 250000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 52 (24.6 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