Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_082109125.1 AL072_RS25760 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_001305595.1:WP_082109125.1 Length = 531 Score = 281 bits (718), Expect = 5e-80 Identities = 173/497 (34%), Positives = 272/497 (54%), Gaps = 24/497 (4%) Query: 4 EDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHK 63 +D I +L ++ E AL GG +++A + KG + ARER+D LD +F E F + Sbjct: 27 QDHIQKLHQQTEHALGMGGPEKLAKRRAKGMLNARERLDVLLDPESFWESGMFGRSIRPE 86 Query: 64 FGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAP 123 G K P DG I G+G +DGR V V ++DFTV G S V +KI + + A + G P Sbjct: 87 MG---EKSPADGKIAGYGRIDGRDVAVVSNDFTVLGASSSAVNGKKIRHMREVASKRGMP 143 Query: 124 VIGLNDSAGARIQEGVQSLGGF------GEIFR-RNTEASGVVPQISAIMGPCAGGAVYS 176 ++ L +S GAR+ + + + G GE R R+T P SA++G C G + + Sbjct: 144 MVFLGESVGARMPDRMGAPGRAMLGQDPGEYLRDRHT------PWASALLGDCYGSSTWY 197 Query: 177 PALTDFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQA 236 ++DF M R + M + V E + ++LGG H+S +G+ D+EE+A Sbjct: 198 ACVSDFVVM-RKGATMAVASSRVTSMAISETIDPEDLGGWRLHSSVTGLVDMVVDSEEEA 256 Query: 237 LDDIRHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEG 296 L +R L YLP + E+ PR + + +D + +++P++ K YD+ DV+N V+D G Sbjct: 257 LQAVRTFLGYLPSHAGEEAPRRPVPEGSDDASDRILDVLPEERTKVYDVRDVINCVVDTG 316 Query: 297 SFFGVQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIP 356 SFF ++ F K+I G R+DG SVG++A+ PRV G +D++A K F+ CDSFN+P Sbjct: 317 SFFELKARFGKSITTGLARIDGRSVGVIASNPRVKGGAIDVDAMRKATGFLVLCDSFNLP 376 Query: 357 ILSFVDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAY-DVMASKH 415 I+ VD PGFL G + E + A S TVP ++V+ RK+YG AY ++ +H Sbjct: 377 IVFLVDQPGFLIGVEGERRWAPGRIMNWMNALSLVTVPKLSVLMRKSYGQAYLNMGGGRH 436 Query: 416 LGADVNYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAAD 475 +D +WPTA++ + P VNIL+ ++ +DDP+ R L +E +++ ++ + A Sbjct: 437 --SDEVLSWPTADLGFVDPAVGVNILH--GIKESDDPERFR-ALYQELQKD-SSAWALAA 490 Query: 476 RGFVDDVIEPGDTRNRL 492 VI+P TR L Sbjct: 491 LYETHAVIDPRATRAAL 507 Lambda K H 0.318 0.138 0.407 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: 665 Number of extensions: 25 Number of successful extensions: 7 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: 516 Length of database: 531 Length adjustment: 35 Effective length of query: 481 Effective length of database: 496 Effective search space: 238576 Effective search space used: 238576 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: 41 (21.7 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