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_012382808.1 BIND_RS19730 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000019845.1:WP_012382808.1 Length = 525 Score = 434 bits (1116), Expect = e-126 Identities = 224/469 (47%), Positives = 305/469 (65%), Gaps = 3/469 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MFSK+L+ANRGEIA+RV+RA +ELG+ TVAV+S AD HV+ A E+ +GP A +SY Sbjct: 1 MFSKILIANRGEIALRVLRAAQELGISTVAVHSTADAEAMHVKLAHESVCLGPPPARESY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I A + A+A+HPGYGFL+ENA FA + ++GP + + +G+K +A+ Sbjct: 61 LNIPAIIAACQITGAEAVHPGYGFLSENAHFAEILAAHNIAFIGPKPEHIRIMGDKIEAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 +P VPG++ + AE+ +A+ G+PV IKA GGGGRG+KV HS DE Sbjct: 121 RTAISLGIPCVPGSSGALNHAEEALDIAEGIGFPVLIKAASGGGGRGMKVAHSRDEFASA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TA E +A F + SVY+EKYLE PRHIE+Q+L D GN HLGERDCSLQRRHQKV E Sbjct: 181 VATASSEAKAAFGDGSVYLEKYLENPRHIEIQVLGDGRGNAVHLGERDCSLQRRHQKVWE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 E+PSP L E RE I E +R Y GT+EFL +DG+FYF+E+NTRIQVEH VTE Sbjct: 241 ESPSPVLDETQREEICEICAVAMRKLGYLGVGTIEFLYKDGKFYFIEMNTRIQVEHPVTE 300 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +TG D+V Q+++AAG+ L QD V + GH++E RINAE P F P+ G + Y P Sbjct: 301 MITGFDLVNEQIKIAAGQPLSIIQDQVVVRGHAIECRINAEDP-TTFTPSPGRIGQYHTP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GGIGIR+D A G +I YDS+I KLIV G +R+E L+R RAL+EF ++G++T IP Sbjct: 360 GGIGIRIDSAAYAGYKIPPTYDSLIGKLIVHGPNRKEALMRLRRALDEFIVDGIKTTIPL 419 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLD--PERIEAAVERWSPEAVAGDEEE 467 + ++ + + G ++ +L+ L E + VE EA DE + Sbjct: 420 FQRLVNNADIQNGQYSIHWLEAFLAAVAEDVVLTVETNMNEAEEADEPD 468 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: 714 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: 525 Length adjustment: 36 Effective length of query: 565 Effective length of database: 489 Effective search space: 276285 Effective search space used: 276285 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: 53 (25.0 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