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 YP_004144552.1 Mesci_5404 carbamoyl-phosphate synthase L chain ATP-binding protein
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000185905.1:YP_004144552.1 Length = 454 Score = 407 bits (1047), Expect = e-118 Identities = 219/443 (49%), Positives = 289/443 (65%), Gaps = 3/443 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 M K+LVANRGEIAVR++RA ++LG+ TVAVYS AD HV+ ADEA NIGP A SY Sbjct: 1 MLKKLLVANRGEIAVRIIRAAQDLGIATVAVYSAADAESLHVQLADEAVNIGPPAAKKSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ E++++AAR D++HPGYGFLAENA F+ V + +VGPS DA+ +G+K AR Sbjct: 61 LNVEAILKAARDTGCDSVHPGYGFLAENAAFSDAVTGAALVFVGPSGDAIRMMGDKVSAR 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 S A VPVVPG+ + E V G+PV IKA GGGGRG+++ +S E + Sbjct: 121 SAAAAAGVPVVPGSAGRVEGLEAGHEVLTATGFPVMIKAAAGGGGRGIRIANSLAEFEQA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 F A+ E A F + +Y+EK + RHIEVQ+LAD + H ER+CSLQRR QKV E Sbjct: 181 FPQAEAEALAAFGDGGLYMEKVIGKARHIEVQVLADGSDAI-HCYERECSLQRRRQKVWE 239 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVED--GEFYFMEVNTRIQVEHTV 298 EAPS ALS+ LRE + +A +A +Y+ AGTVE+L +D FYF+E+NTRIQVEH V Sbjct: 240 EAPSRALSDRLREELCASAVALAKAVKYSGAGTVEYLYDDEADRFYFIEMNTRIQVEHPV 299 Query: 299 TEEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYD 358 TE +TG+D+V LR+A GE+L Q DV ++GH++E R+NAE P KEFAP G ++ Sbjct: 300 TEAITGIDLVAEMLRIAGGEKLRIRQSDVSVKGHAIEVRLNAEDPAKEFAPFPGQVAELR 359 Query: 359 PPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVI 418 PGG G+R D + QG ++ YDS++AKLIV RE +VR RALNE I GL+T Sbjct: 360 IPGGPGVRFDSMLYQGYQVPPFYDSLLAKLIVHAETREAAIVRLIRALNELKIGGLKTTK 419 Query: 419 PFHRLMLTDEAFREGSHTTKYLD 441 P + D A R G T++L+ Sbjct: 420 PLFLALAADPAMRAGDVHTRWLE 442 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: 661 Number of extensions: 28 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: 454 Length adjustment: 35 Effective length of query: 566 Effective length of database: 419 Effective search space: 237154 Effective search space used: 237154 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