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_012854020.1 TCUR_RS18230 ATP-grasp domain-containing protein
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000024385.1:WP_012854020.1 Length = 444 Score = 399 bits (1024), Expect = e-115 Identities = 214/439 (48%), Positives = 284/439 (64%), Gaps = 5/439 (1%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF VLVANRGEIA RV+ +G++ +AVYSEAD V ADEA IGPA A SY Sbjct: 1 MFESVLVANRGEIASRVIHTVRAMGLKAIAVYSEADADLPFVAEADEAILIGPAHPAGSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 LD + V+EAAR+ +A AIHPGYGFLAE+AEFA +V D W+GP A+ R+G+K AR Sbjct: 61 LDADRVLEAARRTNAQAIHPGYGFLAESAEFAERVTDQGLVWIGPPPLAIARMGDKINAR 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 +LM +A VPV G EP A A A+ GYPV +KA GGGGG G+ E E+ Sbjct: 121 NLMIEAGVPVAAGVWEPVPDAATALAEAERIGYPVMVKAAGGGGGIGMGAARDEAELVKV 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 + +A+ E +F N + +E+Y+E RH+EVQIL G V LGERDCS+QRRHQK++E Sbjct: 181 YASARSSAERFFRNPDILLERYVERARHVEVQILGLADGTVVALGERDCSVQRRHQKIVE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFL--VEDGEFYFMEVNTRIQVEHTV 298 E PSP + LR R+ +AA R A Y AGTVEFL V+ GEF F+E+NTR+QVEH + Sbjct: 241 ETPSPGVDAALRARMTQAAVRAGEAVGYRGAGTVEFLLDVDSGEFVFLEMNTRLQVEHPI 300 Query: 299 TEEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYD 358 TE VTG+D+V+ QL +AAGE++ F+ E GH++EFR+ AE P + F P+ G + + Sbjct: 301 TELVTGIDLVEQQLLIAAGEQVTFT--STEARGHAVEFRVCAEDPLR-FLPSPGDIKIWQ 357 Query: 359 PPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVI 418 P G GIR+D +G+ + YDS++AKL V +DR L RA +A+ F IEG +T + Sbjct: 358 EPVGEGIRIDAGYAEGNTVTPFYDSLLAKLCVHAADRPSALRRAAQAVGAFQIEGPKTNL 417 Query: 419 PFHRLMLTDEAFREGSHTT 437 PF +L +E F G++ T Sbjct: 418 PFFIELLGEEEFVAGTYDT 436 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: 658 Number of extensions: 35 Number of successful extensions: 4 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: 444 Length adjustment: 35 Effective length of query: 566 Effective length of database: 409 Effective search space: 231494 Effective search space used: 231494 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