Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate RR42_RS26670 RR42_RS26670 urea carboxylase
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__Cup4G11:RR42_RS26670 Length = 1199 Score = 418 bits (1075), Expect = e-121 Identities = 232/436 (53%), Positives = 286/436 (65%), Gaps = 5/436 (1%) Query: 11 LLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRGD 70 +L+ANRGEIA R +R+ RALGI SVAV+SD DR+A H AD+AV LGG + ADSYL + Sbjct: 5 VLIANRGEIAVRAIRTLRALGIKSVAVYSDADRNAAHARLADVAVPLGGERAADSYLVAE 64 Query: 71 RIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALME 130 R++ AAL +GAQA+ PGYGFLSE+A FA ACE AGL+F+GP + G K A+ L Sbjct: 65 RVLQAALDTGAQAVFPGYGFLSESAAFAEACEAAGLVFIGPTPHQLREFGLKHRARELAA 124 Query: 131 EAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSSA 190 EAGVP+ PG G LE REA RIGYPV+LK+ AGGGG G+ +AEL+ A S Sbjct: 125 EAGVPMTPG-TGLLCSLEQALREAARIGYPVMLKSTAGGGGIGLSRCADDAELSAAFDSV 183 Query: 191 QREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAPA 250 QR + F +E+ L RH+E+Q+F D G + L ERDCS QRR+QKVVEE PA Sbjct: 184 QRLGEQFFKHGGAFIERCLDCARHIEVQIFGDGAGRVVALGERDCSTQRRNQKVVEETPA 243 Query: 251 PGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLD-ERGQFFFMEMNTRLQVEHPVTEAI 309 P L A R A+ AA+R +++ Y AGTVEF+ D ER F+F+E+N RLQVEHPVTE + Sbjct: 244 PHLSAATRHALHRAAIRLGESVRYRSAGTVEFIYDVEREDFYFLEVNARLQVEHPVTELV 303 Query: 310 TGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAAA 369 TGLDLVA ++VA G+AL P G A+E RLYAEDP F P+ G L E A Sbjct: 304 TGLDLVACMLKVAAGDALDWEAISRPPQGAAMEARLYAEDPLKQFQPSPGTL---TEVAF 360 Query: 370 GPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAFL 429 G RVD V G EVS FYDP+LAKLI G TRE AR+RL A LA T +GG+ TNL +L Sbjct: 361 ADGVRVDGWVETGTEVSAFYDPLLAKLIVHGPTREAARKRLAAALAATRLGGIATNLDYL 420 Query: 430 RRILGHPAFAAAELDT 445 R+I+ P F T Sbjct: 421 RQIVDSPEFTTGRAFT 436 Score = 61.2 bits (147), Expect = 3e-13 Identities = 31/71 (43%), Positives = 47/71 (66%), Gaps = 1/71 (1%) Query: 581 HQG-GLSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGE 639 H G ++A M+GS+ +VLV+PG+ V AG L+V+EAMKME ++ AP AG + A+ C G Sbjct: 1128 HDGHAVTAEMSGSVWKVLVQPGEQVRAGQPLLVVEAMKMELTVLAPVAGTLLAMRCRAGS 1187 Query: 640 LVEEGTPLVEL 650 ++ G L + Sbjct: 1188 AIKVGDRLASI 1198 Lambda K H 0.319 0.135 0.397 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: 1779 Number of extensions: 82 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 655 Length of database: 1199 Length adjustment: 43 Effective length of query: 612 Effective length of database: 1156 Effective search space: 707472 Effective search space used: 707472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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