Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_002719660.1 RSPH17029_RS05945 methylcrotonoyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000015985.1:WP_002719660.1 Length = 534 Score = 690 bits (1780), Expect = 0.0 Identities = 335/532 (62%), Positives = 407/532 (76%) Query: 4 IHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTL 63 + S + P+S F+AN A+H +L A+ E A GGG + RH RGKL R+R+ L Sbjct: 3 LSSRVLPSSETFRANRAHHLALIAETAEAAAWAAAGGGPAAQARHAARGKLPPRERVAGL 62 Query: 64 IDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVK 123 +DP S FLEIGA AA+ +YD PAAG++ GIGRV G+ VM++ NDATVKGGTY+P+TVK Sbjct: 63 LDPGSPFLEIGAFAAHGLYDGAAPAAGVIAGIGRVHGQEVMVVCNDATVKGGTYYPMTVK 122 Query: 124 KHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIAC 183 KHLRAQEIA E RLPC+YLVDSGGA LP Q EVFPDRDHFGRIFYNQAQMSA GIPQIA Sbjct: 123 KHLRAQEIAAECRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQAQMSAAGIPQIAV 182 Query: 184 VMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISG 243 VMGSCTAGGAYVPAMSD +IV+ GTIFL GPPLVKAATGE V+AE+LGG +VHTR+SG Sbjct: 183 VMGSCTAGGAYVPAMSDVTIIVRNQGTIFLAGPPLVKAATGEVVSAEDLGGGEVHTRLSG 242 Query: 244 VADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDV 303 VADY A DD ALA+ R + L + PE P +DP EI G++P D R +D+ Sbjct: 243 VADYLAEDDAHALALARRALGQLNRTRPETVAWAAPEDPAHDPEEILGLVPADLRTPWDI 302 Query: 304 REVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELC 363 RE+IAR+VDGSR EFK R+G TLV GFAH+ G PVGI+ANNG+LFSE+A+KGAHF+ELC Sbjct: 303 RELIARLVDGSRFDEFKPRFGETLVTGFAHLMGCPVGIVANNGVLFSEAAIKGAHFVELC 362 Query: 364 CARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYG 423 R+IPL+FLQNITGFMVG++YEN GIA+ GAK+VTAV+ VPK T+++GGSFGAGNYG Sbjct: 363 SQRSIPLIFLQNITGFMVGRRYENEGIARHGAKMVTAVATTAVPKITLLVGGSFGAGNYG 422 Query: 424 MCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILA 483 M GRAY PR LW WPN+RISVMGG QAA VL T+RRD + +G + EE+ F P + Sbjct: 423 MAGRAYSPRFLWTWPNSRISVMGGEQAAGVLATVRRDAIERQGGHWSAEEEAAFKRPTIE 482 Query: 484 KYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 +E++ HP +ASARLWDDG++DP ++R L L L+AA AP+ PTRFG+FRM Sbjct: 483 MFERQSHPLHASARLWDDGIVDPRKSRETLFLSLSAALNAPIAPTRFGLFRM 534 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: 924 Number of extensions: 32 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: 535 Length of database: 534 Length adjustment: 35 Effective length of query: 500 Effective length of database: 499 Effective search space: 249500 Effective search space used: 249500 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 Apr 10 2024. 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