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_035217562.1 G491_RS29305 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000429905.1:WP_035217562.1 Length = 466 Score = 459 bits (1182), Expect = e-134 Identities = 227/448 (50%), Positives = 314/448 (70%), Gaps = 1/448 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L ANRGEIA+RV+RAC+EL + VAVYSEAD HVR ADE+ IGPA +A SY Sbjct: 1 MFKKILAANRGEIALRVIRACKELEIPCVAVYSEADAESLHVRLADESVCIGPAISAKSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L +++I+AA+ ADAIHPGYG+LAE +FA +++ T++GP D + G+K A+ Sbjct: 61 LSIDNIIKAAKDTGADAIHPGYGYLAEKKDFALACQENGITFIGPKPDNLALAGDKIAAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + MQ A VPV P + D+ + K A + GYP+ +KA GGGGGRG+K+ +++EV+ + Sbjct: 121 TAMQKAGVPVTPSSPGGVDTVAEAKEFAKEIGYPIMVKASGGGGGRGIKICFNDEEVEEE 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 F AK EG F N VYVEK+L PRHIE QILAD+ GNV HLGER+CS+QRR+QK++E Sbjct: 181 FPMAKMEGRTAFGNDEVYVEKFLTKPRHIEFQILADKQGNVIHLGERECSIQRRYQKLVE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 E+PSPAL+ +LR +G+AA +A +Y NAGTVEFL++ D FYFME+N+RIQVEH VT Sbjct: 241 ESPSPALTPELRAAMGQAAINAAKAVDYENAGTVEFLLDGDMNFYFMEINSRIQVEHPVT 300 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E VTG+D+VK Q+R+AAG LD++ DD+ + G ++E RINAE PEK F P+ GT+ Y+P Sbjct: 301 ELVTGVDLVKEQIRLAAGGTLDYTFDDLNLRGWAIECRINAEDPEKHFMPSPGTIEDYNP 360 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 P G G+R+D + QG E+ YDS+I KL+ RE + +RAL EF I ++T IP Sbjct: 361 PAGFGVRLDSHLYQGYELPPFYDSLIGKLVAFDLTREGAIQVMKRALKEFIIGPIKTTIP 420 Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLDPE 447 H +++ D+ F+ G+ T ++ + + E Sbjct: 421 LHLIIMDDDEFKAGNFDTSFITKYVPEE 448 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: 684 Number of extensions: 25 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: 466 Length adjustment: 35 Effective length of query: 566 Effective length of database: 431 Effective search space: 243946 Effective search space used: 243946 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