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_01961 CCNA_01961 biotin carboxylase
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Caulo:CCNA_01961 Length = 448 Score = 441 bits (1135), Expect = e-128 Identities = 222/441 (50%), Positives = 303/441 (68%), Gaps = 1/441 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+RV RAC+E+G+ TVAV+SEAD++ VR ADE+ IGPA AA SY Sbjct: 1 MFDKILIANRGEIALRVHRACKEMGIATVAVHSEADRNSMWVRLADESVCIGPAPAAKSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ S+I AA A AIHPGYGFL+ENA FA V FT++GP + + +G+K A+ Sbjct: 61 LNIPSIIAAAEITGAQAIHPGYGFLSENARFAEIVGAHGFTFIGPKPEHIRMMGDKITAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 ++DA +PVVPG+ + E+ A+ G+PV IKA GGGGRG+KV + +++ Sbjct: 121 QAVKDAGIPVVPGSDGGVSTEEEAFEAAEKIGFPVLIKAAAGGGGRGMKVAQTREDLAEA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TA+ E A F + +VY+E+YL+ PRHIE+Q++AD HGNV HLGERDCSLQRRHQKV+E Sbjct: 181 VSTARAEARAAFGDDTVYMERYLQKPRHIELQVIADSHGNVVHLGERDCSLQRRHQKVLE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 EAPSPALS + R +IG+ V+A Y GT+EFL E+ EF+F+E+NTR+QVEH VTE Sbjct: 241 EAPSPALSAEGRAKIGKVVVDAVKAIGYLGVGTIEFLWENDEFFFIEMNTRLQVEHPVTE 300 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +TG+D+V+ Q+R+AAG L F+QDDV EGH++E RINAE + F P+ G ++ + P Sbjct: 301 AITGIDLVREQIRIAAGLPLSFTQDDVVFEGHAIECRINAE-NARTFTPSPGVITDFHAP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG+G+R+D A+ G I YDS+I KLIV G DR E + R +R L E + G+ T IP Sbjct: 360 GGLGVRLDSAIYTGYAIPPYYDSLIGKLIVHGRDRAECIARLKRCLGEMVVGGVETTIPL 419 Query: 421 HRLMLTDEAFREGSHTTKYLD 441 + +L G + +L+ Sbjct: 420 FQDLLVQPDILAGDYNIHWLE 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: 646 Number of extensions: 27 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: 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 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