Align non-biotin containing subunit of 3-methylcrotonyl-CoA carboxylase; EC 6.4.1.4 (characterized)
to candidate RR42_RS18165 RR42_RS18165 carbamoyl-phosphate synthase large subunit
Query= CharProtDB::CH_122289 (587 letters) >FitnessBrowser__Cup4G11:RR42_RS18165 Length = 1112 Score = 190 bits (482), Expect = 3e-52 Identities = 160/513 (31%), Positives = 237/513 (46%), Gaps = 46/513 (8%) Query: 96 HSTISQGGPQKAKDKHVARGKMLPRDRVSALIDPGTSFLELSQLA---GHEVYPGEDV-- 150 H+ +A DKH ARG R+ ++ L D G SF+E LA + ED+ Sbjct: 602 HALTQDAARPQAVDKHHARGGRTARENIAQLCDAG-SFIEYGALAIAAQRQRRSVEDLER 660 Query: 151 --PAGGIITGIGTVEG-------VTCMIVANDSTVKGGTYYPVTVKKHLRAQAIAQENKL 201 PA GI+TGIGTV CM++A D TV GT KK R A+A++ +L Sbjct: 661 ATPADGIVTGIGTVNAERFPATDARCMVLAYDYTVLAGTQGFYGHKKLDRMLALARQWRL 720 Query: 202 PCIYLVDSGGANLPHQADVFPDKEHFGRIFFNQARMSSQGIPQISVVMGPCTAGGAYVPA 261 P + + GG P D F AR+S Q +P + +V G C AG A + Sbjct: 721 PVVLFAEGGGGR-PGDTDTPVVAGLDCTSFIQFARLSGQ-VPLVGIVSGRCFAGNAALLG 778 Query: 262 MSDETIIVENQGTIFLAGPPLVKAATGEVVSAEDLGGGQLHSTISGVTDYLAVDDAHAIV 321 +D II TI + GP +++ V +AE++G + + +GV D L D+ A+ Sbjct: 779 CAD-VIIATRNATIGMGGPAMIEGGGLGVFAAEEVGPVSVQAP-NGVIDVLVDDEIAAVE 836 Query: 322 LARRSISNLNYPKAKQPLESNDDIKEPLYDPAELNGIVGTNLRRQIPVHEVIARIVDGSE 381 ARR +S Y + P D + L ++ N R + V+A + D Sbjct: 837 TARRYLS---YFQGDLPDWEAGDARA-------LRHLIPENRLRSYDMRGVLAALADHDS 886 Query: 382 FAEFKRDYGTTLVTGFARIHGHRVGIVANN-----GILFSESSLKGAHFIELCAQRNIPL 436 E + +G ++T RI G G +ANN G + ++++ K A F++LC +P+ Sbjct: 887 VLELRAAFGAGIITALIRIEGRAFGCIANNPRHLGGAIDADAADKAARFMQLCDAHGLPI 946 Query: 437 VFLQNISGFMVGADAEKGGIAKNGAKLVTAVACADVPKFTVVFGSSAGAGNYGMCGRAYS 496 V L + GFMVG +AEK ++ ++L VP FTVV G G M G ++S Sbjct: 947 VSLCDTPGFMVGPEAEKTATVRHVSRLFVTAGALRVPFFTVVLRKGYGLGAQAMAGGSFS 1006 Query: 497 -PRFLFMWPNAKIGVMGSELS---SVMEAVGRTADPE----LKARI----DRESEATFSS 544 P F WP+ + G MG E S + + ADP+ L AR+ R A + Sbjct: 1007 APFFTAAWPSGEFGAMGIEGSIRLGFRKELEAVADPDEREALFARMIEGAYRRGRALNMA 1066 Query: 545 ARLWDDGIIPPAHTRHVLGLSLAAALGGKSDKD 577 + L D +I PA TRH L LA+AL + +D Sbjct: 1067 SHLEIDAVIDPADTRHWLLRGLASALPASAARD 1099 Lambda K H 0.318 0.134 0.391 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: 1410 Number of extensions: 56 Number of successful extensions: 7 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: 587 Length of database: 1112 Length adjustment: 41 Effective length of query: 546 Effective length of database: 1071 Effective search space: 584766 Effective search space used: 584766 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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