Align propionyl-CoA carboxylase (EC 6.4.1.3) (characterized)
to candidate WP_013075854.1 BTUS_RS09335 acyl-CoA carboxylase subunit beta
Query= metacyc::MONOMER-16260 (572 letters) >NCBI__GCF_000092905.1:WP_013075854.1 Length = 506 Score = 501 bits (1290), Expect = e-146 Identities = 249/494 (50%), Positives = 336/494 (68%), Gaps = 2/494 (0%) Query: 75 EILEGGPEKYKEQLPEEGKLFVRDRIDLWFGDDFLFEDGKFAEFDADDQLPADGLITGAA 134 +IL GG EKY E+L +GKLFVRDR+ L +D FE+G FA A+ LPADG++TG Sbjct: 10 KILGGGEEKYHEKLRRDGKLFVRDRLRLLLDEDISFEEGLFANCQAEG-LPADGVVTGVG 68 Query: 135 EFEGRDLHFMANDYTVKRGSMAAKGVEKFLRMQQRALKTGRPVLYLMDSSGGRIDQQTGF 194 GR + FMAND TVK GS A+ VEK LR+Q+ A K P+LYL+DS+G RI Q Sbjct: 69 RIHGRTVCFMANDSTVKAGSWGARTVEKILRIQELAEKMRVPLLYLVDSAGARITDQVEM 128 Query: 195 FANREGIGKFYYNHSMLSGRVPQICVLYGPCIAGAAYTPVFADFTVMVRDMSAMAIASPR 254 F R G G+ +Y+ LSG +PQIC+L+GP AG AY P F D +MV ++M + SPR Sbjct: 129 FPGRRGAGRIFYHQVRLSGVIPQICLLFGPSAAGGAYIPAFCDLVIMVEGNASMYLGSPR 188 Query: 255 MVEMVTGEEISLEELGGPDIHAQHSGSADLIADDEEHARELVAQLISYLPDNADEDPPQT 314 M EMV GE+++LEE+GG +H SG D++ DE A + + ++P+N E P + Sbjct: 189 MAEMVIGEKVTLEEMGGARMHCSVSGCGDVLVKDEHEAIAAAREYLRFMPNNWQEKPSRA 248 Query: 315 SGTAPKRSPEGIDSVVPEKPNKGYDMFDVIERVVDAGSTLELRPEYGKEIITSFARIDGR 374 PK S + +++PE N ++M+DVI+R+VD GS E++ + +E+IT ARIDGR Sbjct: 249 ECLPPKASERPLSAIIPENQNVPFNMYDVIDRLVDEGSFFEIKRLFAQELITGLARIDGR 308 Query: 375 PIGVIANQPAQRAGAIFPDAAEKAAQFIWTCDAYNIPLLYLCDTPGFMAGSGVEKEGILE 434 P+G++ANQP + G +F D+A+KAA+F+ CDA++IPLL+L D PGFM G+ VE++GI+ Sbjct: 309 PVGIVANQPRVKGGVLFVDSADKAARFVMLCDAFSIPLLFLADVPGFMIGTKVERQGIIR 368 Query: 435 QGKKMIYATSSATVPKQSVVVRKAYGAGIYAMSGPAYDPESTIGLPSGEIAIMGPEAAIN 494 G KMI A S ATVPK SV+VRKAYGAG+YAM+GPA++P++ I LP +IA+MGPEAA+N Sbjct: 369 HGAKMIAAVSEATVPKISVIVRKAYGAGLYAMAGPAFEPDACIALPGAQIAVMGPEAAVN 428 Query: 495 AVYARKLSEIDDEDERQQKEQELREAYREDIDIHRMASEVVVDDIVPPSDLRTELTNRFA 554 AVY+ K+ + E ER QE RE YR DIDI+R+A E+VVD+IV P LR EL RFA Sbjct: 429 AVYSNKIQSL-PEAERPGFIQEKREEYRRDIDIYRLAGELVVDEIVEPDRLREELIKRFA 487 Query: 555 FYETVEKDLPDKKH 568 YET E +KH Sbjct: 488 AYETKELTFARRKH 501 Lambda K H 0.315 0.135 0.385 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: 772 Number of extensions: 35 Number of successful extensions: 5 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: 572 Length of database: 506 Length adjustment: 35 Effective length of query: 537 Effective length of database: 471 Effective search space: 252927 Effective search space used: 252927 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: 42 (22.0 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