Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011777667.1 MVAN_RS01760 acetyl-CoA carboxylase carboxyltransferase subunit
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000015305.1:WP_011777667.1 Length = 532 Score = 509 bits (1310), Expect = e-148 Identities = 276/543 (50%), Positives = 358/543 (65%), Gaps = 19/543 (3%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M+++ S + P S FQ N + A L E+L + GGG +RH +RG+L R+RI Sbjct: 1 MTVLTSDVDPASDTFQFNREVQSAAVAALDEQLRLVADGGGERYVKRHHDRGRLLARERI 60 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120 + L+D D+ F+E+ ALAA+ E A IV G+G V+G MIIA+D TV+GGT P Sbjct: 61 ELLVDRDAPFMELSALAAWGT--EFNVGAAIVTGVGVVSGVECMIIAHDPTVRGGTMNPY 118 Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180 T++K+LRA EIAR NRLP +YLV+SGGA LP QSE+F H G+IF++ ++S+ GIP Sbjct: 119 TLRKNLRALEIARVNRLPVVYLVESGGADLPTQSELFV---HAGKIFHDLTELSSLGIPT 175 Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240 I+ V G+ TAGGAYVP M D V+V +FLGGPPLVK ATGEE E LGGAD+HTR Sbjct: 176 ISLVFGNSTAGGAYVPGMCDYAVLVDKQAKVFLGGPPLVKMATGEESDDESLGGADMHTR 235 Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEP------PRYDPREIYGILP 294 +SG+ DYFA D+ +A+ I RDIVAHL NW P P P YD E+ GI Sbjct: 236 VSGLGDYFAVDETDAIRIGRDIVAHL------NWHKLGPGPTQPADEPLYDVEELLGIAS 289 Query: 295 RDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILAN-NGILFSESA 353 D R +D REVIAR+ DGSR E+K R+GT+L G+A I GFPVGILAN G+LFSE + Sbjct: 290 GDSRVPFDPREVIARVADGSRFSEYKPRWGTSLATGWASIHGFPVGILANTRGVLFSEES 349 Query: 354 LKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVII 413 K FI L + PL+FLQN+TGFMVG +YE GGI KDGAK++ AV+ + VP T+ + Sbjct: 350 KKATEFILLANQTDTPLIFLQNVTGFMVGAEYEQGGIIKDGAKMINAVTNSTVPHITINM 409 Query: 414 GGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEE 473 GGSFGAGNYGM GRAY PR ++ W NA+++VMG Q A VL + + A G++ E Sbjct: 410 GGSFGAGNYGMSGRAYDPRFMFSWVNAKLAVMGAAQLAGVLSIVGKAAAAAAGREFDREA 469 Query: 474 QERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTR-FGV 532 + A I A+ E+E H ++ SAR++DDGVIDP +TR VL + L+AA V+ R FGV Sbjct: 470 DAKRTAEIEAQIEKESHSFFVSARIYDDGVIDPRDTRSVLGMALSAAHSNVVEGRRGFGV 529 Query: 533 FRM 535 FRM Sbjct: 530 FRM 532 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: 785 Number of extensions: 30 Number of successful extensions: 4 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: 532 Length adjustment: 35 Effective length of query: 500 Effective length of database: 497 Effective search space: 248500 Effective search space used: 248500 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 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