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 PfGW456L13_52 Biotin carboxylase of acetyl-CoA carboxylase (EC 6.3.4.14)
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_52 Length = 452 Score = 442 bits (1137), Expect = e-128 Identities = 224/446 (50%), Positives = 301/446 (67%), Gaps = 2/446 (0%) Query: 4 KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63 KVL+ANRGEIA+R++RAC+E+G++TVAVYS+ADK H+ ADE+ IGPA AA SYL Sbjct: 7 KVLIANRGEIALRILRACKEMGIKTVAVYSKADKELMHLGLADESVCIGPASAAHSYLHI 66 Query: 64 ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123 ++I AA A AIHPGYGFLAENA+FA +VE S F ++GP A+ + +G+K A+ M Sbjct: 67 PAIIAAAEVTGATAIHPGYGFLAENADFAEQVEKSGFAFIGPKAETIRLMGDKVSAKHAM 126 Query: 124 QDADVPVVPGTTEPADSAEDVKA-VADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFE 182 A VP VPG+ P E+ + + GYPV IKA GGGGGRG++VVH E+++ + Sbjct: 127 IAAGVPTVPGSDGPLPEDEETALRIGREVGYPVIIKAAGGGGGRGMRVVHKEEDLIASAK 186 Query: 183 TAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEA 242 + E A F N VY+EK+L PRH+EVQ+L+D G HLG+RDCSLQRRHQKV+EEA Sbjct: 187 LTRSEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGQAIHLGDRDCSLQRRHQKVLEEA 246 Query: 243 PSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTEEV 302 P+P + E+ RE + R Y AGT EFL E+G FYF+E+NTR+QVEH V+E V Sbjct: 247 PAPGIDENAREEVLARCVRACIDIGYRGAGTFEFLYENGRFYFIEMNTRVQVEHPVSEMV 306 Query: 303 TGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPGG 362 TG+D+VK L +AAG +L F+QDDV I GH++E RINAE P K F P+ GT+ + PGG Sbjct: 307 TGIDIVKEMLSIAAGNKLSFTQDDVVIRGHALECRINAEDP-KTFMPSPGTVKHFHAPGG 365 Query: 363 IGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPFHR 422 G+R+D + G + +YDS+I KLI G+ R+E + R AL+E ++G++T IP HR Sbjct: 366 NGVRVDSHLYSGYAVPPNYDSLIGKLITYGATRDEAMARMRNALDEIVVDGIKTNIPLHR 425 Query: 423 LMLTDEAFREGSHTTKYLDEVLDPER 448 + DE F +G YL+ L E+ Sbjct: 426 DLTRDEGFCKGGVNIHYLEHKLAGEK 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: 652 Number of extensions: 22 Number of successful extensions: 3 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: 452 Length adjustment: 35 Effective length of query: 566 Effective length of database: 417 Effective search space: 236022 Effective search space used: 236022 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