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 GFF3994 HP15_3934 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Marino:GFF3994 Length = 473 Score = 426 bits (1095), Expect = e-123 Identities = 224/460 (48%), Positives = 305/460 (66%), Gaps = 5/460 (1%) Query: 4 KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63 K+L+ANRGEIAVR+ RAC ELG+R+VA++SEAD++ HV+ ADEAY I + YL+ Sbjct: 5 KLLIANRGEIAVRIARACSELGIRSVAIHSEADEYSLHVKKADEAYQISKDPLS-GYLNP 63 Query: 64 ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123 ++ A + DA+HPGYGFL+ENAE A E T+VGPSA+A+ +G+KT+AR Sbjct: 64 HHIVNMAVETGCDALHPGYGFLSENAELAAICEQRGITFVGPSANAISSMGDKTQARQTA 123 Query: 124 QDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFET 183 A VPV PG+ ED A D GYPV +KA GGGGRG++ +E E+ FE Sbjct: 124 LAAGVPVTPGSEGNLADVEDAVVQAADIGYPVMLKATSGGGGRGIRRCDNEKELRQNFER 183 Query: 184 AKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEAP 243 E F +A V++EK + PRHIEVQILAD HGNV HL ERDCS+QRR+QK+IE AP Sbjct: 184 VISEATKAFGSAEVFLEKCIIEPRHIEVQILADTHGNVVHLYERDCSIQRRNQKLIELAP 243 Query: 244 SPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVTEEV 302 SP L E RE IG+ A+R + Y NAGTVEFL++ DG FYFME+NTR+QVEHT+TEE+ Sbjct: 244 SPQLEESQREYIGDLAKRVAKQCGYVNAGTVEFLLDHDGSFYFMEMNTRVQVEHTITEEI 303 Query: 303 TGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPGG 362 TG+D++K Q+R+AAGE L Q+D+ G + +FRINAE P+ F P+ G +S Y GG Sbjct: 304 TGVDIIKAQIRIAAGEPLGLKQEDISYRGFAAQFRINAEDPKNGFLPSFGRISRYYSAGG 363 Query: 363 IGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPFHR 422 G+R D + G EI YDSM AKLIV D +E++ R+ RAL + I G++T IP+++ Sbjct: 364 PGVRTDANMYTGYEIPPYYDSMCAKLIVWAMDWDELIARSRRALGDMGIYGVQTTIPYYK 423 Query: 423 LMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVA 462 +L F+ T +++ +P+ +E + + PE++A Sbjct: 424 QILEHPDFQAADFNTGFVER--NPQLLEYS-SKTRPESIA 460 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: 619 Number of extensions: 20 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: 473 Length adjustment: 35 Effective length of query: 566 Effective length of database: 438 Effective search space: 247908 Effective search space used: 247908 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