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_025762799.1 X939_RS0108310 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000566685.1:WP_025762799.1 Length = 448 Score = 446 bits (1148), Expect = e-130 Identities = 224/442 (50%), Positives = 312/442 (70%), Gaps = 3/442 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+RV+R C E+G++TVAVYS AD+ HVR+ADEA IGP + SY Sbjct: 1 MFKKILIANRGEIALRVIRTCREMGIKTVAVYSTADRDSLHVRFADEAVCIGPPMSKLSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ +++I AA ADAIHPGYGFL+ENAEF++ D ++G +A + +G+K A+ Sbjct: 61 LNIQNIISAAEVTGADAIHPGYGFLSENAEFSQICADYGIKFIGATAAQINGMGDKATAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + M A VPVVPG+ +S E K +A+ GYPV +KA GGGGRG+++++ ++ + Sbjct: 121 ATMIKAGVPVVPGSEGLLESVEQGKRLAEGIGYPVIVKATAGGGGRGMRIINKPEDFEKA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 + A+ E A F N +Y+EK++E PRHIE+QI+ D+ G V HL ERDCS+QRRHQK++E Sbjct: 181 WTDARTESAAAFGNDGLYLEKFVEEPRHIEIQIVGDQFGTVCHLSERDCSIQRRHQKLVE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 E PSP ++ +LRE++G AA +G +A Y AGTVEFLV+ G+FYFME+NTRIQVEH +T Sbjct: 241 ETPSPIITPELREKMGAAAIKGAQAIGYEGAGTVEFLVDKHGDFYFMEMNTRIQVEHPIT 300 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 EEVT D++K Q++VAAGE + S + + ++ME RINAE P F P+ G ++ Sbjct: 301 EEVTNFDLIKEQIKVAAGEPI--SGVNYIPQLYAMECRINAEDPGNGFRPSPGKITNLHF 358 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG G+R+D V G I +YDSMIAK+IV+G REEV+ R +RAL EF +EG++T IP Sbjct: 359 PGGHGVRIDSHVYSGYTIPPNYDSMIAKVIVSGQSREEVITRMKRALQEFVLEGIKTTIP 418 Query: 420 FHRLMLTDEAFREGSHTTKYLD 441 FH ++ D F+ G+ TTKYL+ Sbjct: 419 FHIKLMDDPGFKSGNFTTKYLE 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: 617 Number of extensions: 23 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: 448 Length adjustment: 35 Effective length of query: 566 Effective length of database: 413 Effective search space: 233758 Effective search space used: 233758 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