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 RR42_RS17700 RR42_RS17700 acetyl-CoA carboxylase
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Cup4G11:RR42_RS17700 Length = 455 Score = 441 bits (1135), Expect = e-128 Identities = 221/450 (49%), Positives = 305/450 (67%), Gaps = 2/450 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+R+ RAC ELG++TV VYSEADK +V+ ADEA IGPA + SY Sbjct: 1 MFEKILIANRGEIALRIQRACRELGIKTVVVYSEADKEAKYVKLADEAVCIGPAPSPLSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA DA AIHPGYGFL+ENA+FA +VE S F ++GP+++++ +G+K A+ Sbjct: 61 LNMPAIISAAEVTDAQAIHPGYGFLSENADFAERVEKSGFVFIGPTSESIRLMGDKVSAK 120 Query: 121 SLMQDADVPVVPGTTEPA-DSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179 M + VP VPG+ D +++ A A GYPV IKA GGGGGRG++VVH+E + Sbjct: 121 QAMIKSGVPCVPGSEGALPDDPKEILATARAVGYPVIIKAAGGGGGRGMRVVHTEAALVN 180 Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239 + E F N VY+EK+LE PRH+E+QILAD+H LGERDCS+QRRHQKVI Sbjct: 181 AVNMTREEAGRAFGNPEVYMEKFLENPRHVEIQILADQHRQAIWLGERDCSMQRRHQKVI 240 Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299 EEAP+P + L ERIG+ + Y AGT EFL E+ EFYF+E+NTR+QVEH VT Sbjct: 241 EEAPAPHIPRRLIERIGDRCAEACKKIGYRGAGTFEFLYENNEFYFIEMNTRVQVEHPVT 300 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E +TG+D+V+ Q+R+A GE+L + Q DV++ GHS+E RINAE P K F P+ G ++ + Sbjct: 301 EMITGIDIVQEQIRIAFGEKLRWRQKDVQLRGHSIECRINAEDPFK-FTPSPGRITAWHM 359 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG G+R+D G + +YDSMI K+I G+ RE+ + R AL+E ++G++T +P Sbjct: 360 PGGPGVRVDSHAYDGYFVPPNYDSMIGKIITYGATREQAIARMRIALSEMVVDGIQTNVP 419 Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLDPERI 449 HR ++ D F EG + YL+ L + + Sbjct: 420 LHRELMLDANFVEGGTSIHYLEHRLAQKNV 449 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: 617 Number of extensions: 21 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: 455 Length adjustment: 35 Effective length of query: 566 Effective length of database: 420 Effective search space: 237720 Effective search space used: 237720 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 17 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