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 GFF4012 Psest_4085 Biotin carboxylase
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__psRCH2:GFF4012 Length = 471 Score = 419 bits (1077), Expect = e-121 Identities = 214/455 (47%), Positives = 298/455 (65%), Gaps = 3/455 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 M K+L+ANRGEIAVR++RAC E+GVR+VAV+SEAD+H HV+ ADEA+ IG A Y Sbjct: 1 MIKKLLIANRGEIAVRIVRACAEMGVRSVAVFSEADRHALHVKRADEAHFIGEDPLA-GY 59 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++ A + DA+HPGYGFL+ENAE A + +VGPSA+ + R+G+KT+AR Sbjct: 60 LNPRKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFVGPSAEVIRRMGDKTEAR 119 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 M A VPV PGT + A+ GYPV +KA GGGGRG++ +S+ E++ Sbjct: 120 RSMIKAGVPVTPGTEGNVRDLAEALREAERIGYPVMLKATSGGGGRGIRRCNSQAELESA 179 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 + E F +A V++EK + P+HIE QILAD GN HL ERDCS+QRR+QK+IE Sbjct: 180 YPRVISEATKAFGSAEVFLEKCIVEPKHIEAQILADSFGNTVHLFERDCSIQRRNQKLIE 239 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 APSP L+ + R IG+ A R +A Y NAGTVEFL+ DGE YFME+NTR+QVEHT+TE Sbjct: 240 IAPSPQLTPEQRAYIGDLAVRAAKAVGYENAGTVEFLLADGEVYFMEMNTRVQVEHTITE 299 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 E+TG+D+V+ Q+R+A+G+ L Q+D++ G S++FRINAE P F P G ++ Y P Sbjct: 300 EITGIDIVREQIRIASGQPLSVKQEDIQHRGFSLQFRINAEDPRNNFLPCFGKITRYYAP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG G+R D A+ G I YDSM KL+V EE L R RAL++ ++G++T + Sbjct: 360 GGPGVRTDTAIYTGYTIPPYYDSMCLKLVVWALTWEEALARGSRALDDMRVQGVKTTATY 419 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVER 455 ++ +L + FR G T ++D PE + +++R Sbjct: 420 YQQILANPDFRSGQFNTSFVDN--HPELLNYSIKR 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: 634 Number of extensions: 25 Number of successful extensions: 2 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: 471 Length adjustment: 35 Effective length of query: 566 Effective length of database: 436 Effective search space: 246776 Effective search space used: 246776 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