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_012335126.1 M446_RS26205 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000019365.1:WP_012335126.1 Length = 451 Score = 450 bits (1157), Expect = e-131 Identities = 226/452 (50%), Positives = 305/452 (67%), Gaps = 1/452 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+RV+RA +ELG+ TVAV+S AD HVR ADE+ IGP A DSY Sbjct: 1 MFDKILIANRGEIALRVLRAAKELGIATVAVHSTADADAMHVRLADESVCIGPPPARDSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ S+I A ADA+HPGYGFL+ENA FA + ++GP A+ + +G+K +A+ Sbjct: 61 LNIPSIIAACEITGADAVHPGYGFLSENARFAEVLGHHRIAFIGPKAEHIRVMGDKIEAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 +P VPG+ ++ + VA + GYPV IKA GGGGRG+KV SE++++ Sbjct: 121 RTATRLGIPCVPGSEGGVSDPDEARRVAAEIGYPVLIKAASGGGGRGMKVARSEEDLETA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TA+ E +A F + +VY+EKYLE PRHIEVQ+L D G HL ERDCSLQRRHQKV E Sbjct: 181 LATARIEAKAAFGDDAVYIEKYLEKPRHIEVQVLGDGRGGAIHLAERDCSLQRRHQKVWE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 E PSPAL+ ++RE+IG R ++ YT AGT+EFL EDG FYF+E+NTRIQVEH VTE Sbjct: 241 EGPSPALNPEMREQIGSICARAMQELGYTGAGTIEFLYEDGAFYFIEMNTRIQVEHPVTE 300 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +TG+D+V Q+RVAAG L Q+DV +EGH++E RINAE P F P+ GT++ + PP Sbjct: 301 MITGIDLVNEQIRVAAGAPLSLRQEDVRVEGHAIECRINAEHP-ATFRPSPGTITYFHPP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG+G+R+D A QG I YDS++ KLIV G R E L+R RAL+EF ++G+ T +P Sbjct: 360 GGLGVRVDSAAFQGYRIPPHYDSLVGKLIVHGRTRTECLMRLRRALDEFVVDGIDTTLPL 419 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERIEAA 452 R ++ + + G + +L+E L ++ A Sbjct: 420 FRTLVRNPDIQNGLYDIHWLEEFLRTGGLDVA 451 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: 678 Number of extensions: 28 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: 451 Length adjustment: 35 Effective length of query: 566 Effective length of database: 416 Effective search space: 235456 Effective search space used: 235456 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