Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_053937342.1 WG78_RS08300 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_001294205.1:WP_053937342.1 Length = 459 Score = 465 bits (1197), Expect = e-135 Identities = 234/456 (51%), Positives = 331/456 (72%), Gaps = 6/456 (1%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF+K+L+ANRGEIA+RV+RAC E+G++TV V+SE D+ +V+ ADE+ IGP +A SY Sbjct: 1 MFNKILIANRGEIALRVLRACREMGIKTVVVHSEIDREAKYVKLADESVCIGPNPSAQSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ S+I AA +A+AIHPGYGFL+ENA+FA++VE+S F ++GP+ +++ +G+K A+ Sbjct: 61 LNIPSLIAAAEVTEAEAIHPGYGFLSENADFAQRVEESGFVFIGPTPESIRLMGDKVSAK 120 Query: 121 SLMQDADVPVVPGTTE--PADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVD 178 + M+ A VP VPG+ P D A +K + + GYPV IKA GGGGGRG++VVH+E+E+ Sbjct: 121 NAMKAAGVPCVPGSDGALPDDDASVLK-LGREVGYPVIIKAAGGGGGRGMRVVHAEEELL 179 Query: 179 GQFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKV 238 E K E ++ F N VY+EK+L+ PRHIE+Q+LAD+HG+ +LGERDCS+QRRHQKV Sbjct: 180 RSVEMTKSEAQSAFGNPVVYMEKFLQNPRHIEIQVLADQHGHAIYLGERDCSMQRRHQKV 239 Query: 239 IEEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTV 298 IEEAP+P +++ R+R+GEA R Y AGT EFL E+GEFYF+E+NTR+QVEH V Sbjct: 240 IEEAPAPGITDAQRKRVGEACAEACRKIGYRGAGTFEFLFENGEFYFIEMNTRVQVEHPV 299 Query: 299 TEEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYD 358 TE +TG+D+V+ Q+RVAAGE+L ++Q DV+++GH+ME RINAE P K F P+ G +++Y Sbjct: 300 TELITGIDIVQEQIRVAAGEQLRYTQKDVKLKGHAMECRINAEDPLK-FVPSPGRITSYH 358 Query: 359 PPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVI 418 PGG G+R+D V QG + +YDSMI K+I G RE+ + R AL+E ++G+ T I Sbjct: 359 APGGPGVRVDSHVYQGYFVPPNYDSMIGKIITYGDTREQAMARMRIALSETVVQGIHTNI 418 Query: 419 PFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVE 454 P H+ +L D F +G + YL+ + PE I A VE Sbjct: 419 PLHQQLLLDAEFIKGGTSIHYLEHKM-PE-IRALVE 452 Lambda K H 0.312 0.132 0.371 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: 658 Number of extensions: 26 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: 601 Length of database: 459 Length adjustment: 35 Effective length of query: 566 Effective length of database: 424 Effective search space: 239984 Effective search space used: 239984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 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