Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_073038419.1 BUB04_RS07710 propionyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_900129305.1:WP_073038419.1 Length = 533 Score = 417 bits (1072), Expect = e-121 Identities = 232/526 (44%), Positives = 318/526 (60%), Gaps = 10/526 (1%) Query: 18 NFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSSFLEIGALA 77 N A+ ++ L ER+ Q GG +R ++GK VR I LIDP + F E+ LA Sbjct: 8 NRAFWENEELKLDERVYQAMWPGGEAAVQRLAKQGKQPVRQLIQKLIDPGTEFYELSRLA 67 Query: 78 AYNVYD---EEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQEIARE 134 + ++ E+VP GIV G+G++ G MIIAND+ VK GTYFP+T+KKH+RAQ IA + Sbjct: 68 GFGMHYPGVEDVPCGGIVTGLGKIYGNWTMIIANDSRVKAGTYFPITLKKHMRAQAIAEQ 127 Query: 135 NRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCTAGGAY 194 L C+Y+ DSGGA+LP+Q++VFPD HFG +FYN A+MSA+G+ QI G TAGGAY Sbjct: 128 CGLNCVYIADSGGAFLPMQADVFPDDGHFGSMFYNMARMSAKGLKQITLSTGGNTAGGAY 187 Query: 195 VPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFANDDRE 254 + M+ + V++ FLGGPPLVKAATGE ++AE+LGGA VHT+ISG AD+F E Sbjct: 188 IVFMACQAVMIDRMAYSFLGGPPLVKAATGEVISAEDLGGARVHTQISGGADHFCRTQDE 247 Query: 255 ALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIARIVDGS 314 A+ VR+I++ P++ + PP+ IY LP Q +VR +I I D S Sbjct: 248 AIEKVREILSLERPQELQIHRYAE-SPPQVPVETIYEELPAKIHQGINVRNIIRAIADDS 306 Query: 315 RLHEFKTRY----GTTLVCGFAHIEGFPVGILANN--GILFSESALKGAHFIELCCARNI 368 E+K Y G +V G ++G PVGI+A+N GI+F E+A K +I C Sbjct: 307 HFIEYKRNYAPGRGDNIVTGKIRLKGIPVGIIASNGLGIIFVEAARKATEWIVRCSQEKT 366 Query: 369 PLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMCGRA 428 PL+F+Q+ G+MVG + E+ GI K GA +V AVSCA VP+ ++IG GA NYGMCGRA Sbjct: 367 PLLFIQSSPGYMVGSESEHMGIGKYGADMVRAVSCAQVPRIQLVIGPDNGAANYGMCGRA 426 Query: 429 YQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKYEQE 488 Y+P L+ AR SVM G AA VLLTI A G+ M+ E++ F ++ KY+ E Sbjct: 427 YRPHFLFSTMRARTSVMSGRSAAEVLLTIEERKREAEGRPMSEGEKQAFRQQMIEKYDGE 486 Query: 489 GHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFR 534 HP++ ARL +D V+ E R LA+ + P+ FG R Sbjct: 487 AHPFFCGARLLNDRVLKFREIRDWLAVAFEVSLLKPIGEPAFGNLR 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: 820 Number of extensions: 39 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: 533 Length adjustment: 35 Effective length of query: 500 Effective length of database: 498 Effective search space: 249000 Effective search space used: 249000 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