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 Echvi_0191 Echvi_0191 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Cola:Echvi_0191 Length = 449 Score = 447 bits (1150), Expect = e-130 Identities = 223/442 (50%), Positives = 315/442 (71%), Gaps = 3/442 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF+K+L+ANRGEIA+R++R C+E+G++TVAVYS ADK HVR+ADEA IG A + +SY Sbjct: 1 MFNKILIANRGEIALRIIRTCKEMGIKTVAVYSTADKDSLHVRFADEAVCIGAAPSRESY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ VI AA +ADAIHPGYGFL+ENAEF++ E+ ++G S++ ++++G+K A+ Sbjct: 61 LNIPRVIAAAEITNADAIHPGYGFLSENAEFSKICEEYNIKFIGASSEMIDKMGDKATAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + M+ A VP +PG+ DS E +A++ GYPV +KA GGGGRG+++V E E Sbjct: 121 ATMKAAGVPTIPGSEGLLDSIEQGIKIANEMGYPVILKATAGGGGRGMRIVREEKEFKKA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 ++ A++E A F N +Y+EK++E PRHIE+Q++ D G HL ERDCS+QRRHQK++E Sbjct: 181 WDDARQESGAAFGNDGLYLEKFVEEPRHIEIQVVGDNTGKACHLSERDCSIQRRHQKLVE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 E PSP ++++LR+ +G+AA +G A Y AGT+EFLV+ FYFME+NTRIQVEH +T Sbjct: 241 ETPSPFITDELRDAMGKAAIKGAEAIGYEGAGTIEFLVDKHRNFYFMEMNTRIQVEHPIT 300 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 EEVT D++K Q++VAAG + S + + ++ME RINAE P F P+ G ++ Sbjct: 301 EEVTDYDLIKEQIKVAAG--IPISGQNYYPKLYAMECRINAEDPANGFRPSPGKINNLHL 358 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG G+R+D V G I +YDSMIAKLIV+G REEV+VR +RAL EF I+G++T IP Sbjct: 359 PGGRGVRVDSHVYAGYIIPPNYDSMIAKLIVSGQSREEVIVRMKRALEEFVIDGIKTTIP 418 Query: 420 FHRLMLTDEAFREGSHTTKYLD 441 FH +L DE F+ G+ TTK+L+ Sbjct: 419 FHIALLEDEQFKAGNFTTKFLE 440 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: 612 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: 449 Length adjustment: 35 Effective length of query: 566 Effective length of database: 414 Effective search space: 234324 Effective search space used: 234324 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