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_011654459.1 RL_RS29585 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000009265.1:WP_011654459.1 Length = 461 Score = 404 bits (1038), Expect = e-117 Identities = 211/448 (47%), Positives = 286/448 (63%), Gaps = 2/448 (0%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYL 61 F VL+ANRGEIAVR+ RAC ELG++TVA+ SEAD+ + AD +IGP+ AA SYL Sbjct: 13 FDTVLIANRGEIAVRIQRACRELGLKTVAICSEADREAPYGSAADSFLSIGPSSAAKSYL 72 Query: 62 DHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARS 121 + ++++ AAR A A AIHPGYGFL+ENA FA VE + ++GP+A ++ +G+K A+ Sbjct: 73 NQDAILLAARLAGAGAIHPGYGFLSENAAFADAVEKAGLIFIGPTASSIAIMGDKISAKR 132 Query: 122 LMQDADVPVVPGT-TEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 M A VP VPG T D A ++ +A + GYPV +KA GGGGGRG++VV D + Sbjct: 133 AMMAAGVPCVPGPDTALPDDAATIERIALEIGYPVIVKASGGGGGRGMRVVPKADLLHEA 192 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 + E F + S+Y+EK+LE PRHIE+Q++ D+HGN LG RDCS+QRRHQKV+E Sbjct: 193 IALTREEARKAFGSPSLYMEKFLEHPRHIEIQVICDDHGNAVWLGHRDCSMQRRHQKVVE 252 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 EAP+ ++ D+ + +G A + Y GT EFL EDG FYF+E+NTR+QVEH VTE Sbjct: 253 EAPAAGIAPDIIQPVGMACVQACLQIGYRGVGTFEFLYEDGAFYFIEMNTRLQVEHPVTE 312 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +G+D+V+ Q+R A G LD +Q DV EGHS E RINAE PE F P+ G ++ P Sbjct: 313 MTSGVDIVQAQIRAAQGHVLDLTQGDVTCEGHSFECRINAEDPE-TFLPSAGVVTHLALP 371 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 G G+R+D + G ++ YDS+IAKLIV R E + R AL ++EG+ T I F Sbjct: 372 AGPGMRVDTHIHAGYKVSPYYDSLIAKLIVHAPTRAEAMTRMREALAGTEVEGISTNISF 431 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPER 448 R + D AF G YL++ L R Sbjct: 432 LRALFEDGAFARGETDIHYLEQWLKLRR 459 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: 603 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: 461 Length adjustment: 35 Effective length of query: 566 Effective length of database: 426 Effective search space: 241116 Effective search space used: 241116 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