Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate H281DRAFT_03840 H281DRAFT_03840 urea carboxylase
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__Burk376:H281DRAFT_03840 Length = 1199 Score = 400 bits (1029), Expect = e-115 Identities = 211/451 (46%), Positives = 290/451 (64%), Gaps = 10/451 (2%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF K+LIANRG IACRI+RT R L + V+V+S+AD + HV+ A A +G PAA +Y Sbjct: 1 MFEKILIANRGAIACRILRTLRELNVTGVSVFSEADRASRHVSEAPIAHELGDGPAAMTY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L S I++ AR G QAIHPGYGFLSENA F EA AG+ F+GP PA +RA GLK A+ Sbjct: 61 LDSTKILEIARCEGVQAIHPGYGFLSENAAFGEACEAAGIAFIGPTPAQLRAFGLKHTAR 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 + GVP++ G G +D + A IGYPV++K+ AGGGG GMR ++ Sbjct: 121 EIAGEQGVPMLNG-TGLLEDLPAALNAAESIGYPVMLKSTAGGGGIGMRVCWHADELSAH 179 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 +A +R E+ F D V LE+Y+ + RH+E+QVFGD G+ + L RDCS+QRR+QKV+E Sbjct: 180 FDAVKRLGENNFSDSGVFLEKYIERARHLEVQVFGDGKGDAIALGVRDCSVQRRNQKVLE 239 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 E PAP + + +A+ DAAV+ A+A+ Y AGTVEF+ D T FYF+E+NTRLQV Sbjct: 240 ETPAPCLPEGIAQALCDAAVKLAKAVDYRSAGTVEFVYDST----AQQFYFLEVNTRLQV 295 Query: 301 EHPVTEAITGIDLVEWQLRVASG--EPLPKKQADISMNGWAFEARLYAEDPARGFLPATG 358 EH VTE + G+DLV W + +A+G PL + A ++ G A +ARLYAEDP R F+P+ G Sbjct: 296 EHGVTEQVWGVDLVRWMIELAAGTLAPLNELAASLTPRGHAIQARLYAEDPGRDFIPSPG 355 Query: 359 RLTELSFPEGTS---RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECR 415 LT ++FP+ R+D+ + G + PY+DP++AK+I R A L DAL+ R Sbjct: 356 LLTHVAFPQADGSALRIDTWIESGCEVPPYFDPMLAKIIAWSPTREEARHALNDALQNTR 415 Query: 416 IGGTVTNRDFLIRLTEEHDFRSGHPDTGLID 446 I G TNRD+L ++ ++ F SG P T ++ Sbjct: 416 IFGVETNRDYLRQILDDEPFASGEPWTRCLE 446 Score = 42.0 bits (97), Expect = 2e-07 Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 3/69 (4%) Query: 582 QSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHV 641 + E++ D +A G + V+V GD V L+++E+MKME+++ A GT+ ++V Sbjct: 1125 EDGEVSVDSEIA---GSLWQVKVKPGDVVAADDILLIIESMKMEISVCAPCAGTVGEIYV 1181 Query: 642 AEGAQVSEG 650 G+ V G Sbjct: 1182 GPGSPVRAG 1190 Lambda K H 0.319 0.135 0.394 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: 1944 Number of extensions: 98 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 662 Length of database: 1199 Length adjustment: 43 Effective length of query: 619 Effective length of database: 1156 Effective search space: 715564 Effective search space used: 715564 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