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 CCNA_03320 CCNA_03320 biotin carboxylase
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Caulo:CCNA_03320 Length = 1078 Score = 359 bits (922), Expect = e-103 Identities = 238/611 (38%), Positives = 331/611 (54%), Gaps = 82/611 (13%) Query: 3 SKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLD 62 S+VL+ANRGEIAVR+ R E G+ +VA+Y+ D HV AD A + P A +YLD Sbjct: 4 SRVLIANRGEIAVRIARTAAEAGLESVAIYAADDAQSPHVSAADHAVAL-PGAGARAYLD 62 Query: 63 HESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSL 122 +V+ AA+ DA+HPGYGFL+EN AR ++ ++GPS + + G+K AR+L Sbjct: 63 IAAVVAAAKAQGCDALHPGYGFLSENPHLARACAEAGIVFIGPSPEHLTTFGDKAAARAL 122 Query: 123 MQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFE 182 + +P++PGT A + E +A ++G + +KA GGGGRG+++V E+D F Sbjct: 123 AAERGLPLIPGTG--AITLEAARAFQAEHG-AIMLKARAGGGGRGMRMVLDPGELDAAFA 179 Query: 183 TAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEA 242 +RE A F + +Y EK +E RHIEVQI+ D V LG+RDCSLQRR+QK++E A Sbjct: 180 ACEREALAAFGDGGLYAEKLIERARHIEVQIVGDGD-QVLALGDRDCSLQRRNQKLVEIA 238 Query: 243 PSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-------DGEFYFMEVNTRIQVE 295 P+ AL ++LR + + R A Y TVEFLV+ GE +F+EVN R+QVE Sbjct: 239 PA-ALPDNLRAALAGWSER--LCAGYRGLATVEFLVDADPHSPSGGEAFFIEVNPRLQVE 295 Query: 296 HTVTEEVTGLDVVKWQLRVAAGE---ELDFSQDDVEIEGHSMEFRINAEA--PEKEFAPA 350 HTVTEEVTGLD+V+ Q +AAG+ EL+ + G +++ RINAE PE + P+ Sbjct: 296 HTVTEEVTGLDLVRLQFDLAAGKRLGELELTNTPPPF-GVAIQARINAETLTPEGQVRPS 354 Query: 351 TGTLSTYDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFD 410 TGTLS + PPGG G+R+D V G IG YDS++AK+IV G E R +RAL E Sbjct: 355 TGTLSAWTPPGGPGVRVDAGVAAGLTIGAAYDSLLAKVIVRGRTPSEAASRLDRALTELK 414 Query: 411 IEGLRTVIPFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEV 470 + G+ T P R +L G TT ++ + E + A +R +PE A V Sbjct: 415 VAGVATTAPLVRAILAHPTAVTGEATTTFIAQ--HAETLAAEAQRLTPETTA------SV 466 Query: 471 TERTFTVEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQQVIEG 530 T RFEV L GA Sbjct: 467 T-----------RFEV-----------LAGA----------------------------- 475 Query: 531 DGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDS 590 E V A + T+ A+ + EGD V PG + +LEAMKME+ V A GG V +++V G + Sbjct: 476 --EPVVAPLAATVGAITIREGDLVRPGQALAVLEAMKMEHLVSASAGGRVVKIVVQGGAT 533 Query: 591 VDMGDVLLVLE 601 V G L+ LE Sbjct: 534 VAEGQPLVFLE 544 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: 1330 Number of extensions: 56 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 601 Length of database: 1078 Length adjustment: 41 Effective length of query: 560 Effective length of database: 1037 Effective search space: 580720 Effective search space used: 580720 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: 55 (25.8 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