Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 3607893 Dshi_1301 Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__Dino:3607893 Length = 661 Score = 682 bits (1761), Expect = 0.0 Identities = 370/656 (56%), Positives = 446/656 (67%), Gaps = 14/656 (2%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF ++LIANRGEIACR+I T RRLG++TVAV+SD D A HVA+AD A+ +GGA +SY Sbjct: 1 MFERILIANRGEIACRVIDTCRRLGVQTVAVHSDVDAGARHVAMADMAVNLGGAAPRDSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L I+ AAR+ GA+AIHPGYGFLSEN DF EAVA AG++F+GP AAIRAMGLKDAAK Sbjct: 61 LRGEAIIAAARATGAEAIHPGYGFLSENPDFVEAVAAAGLVFIGPSAAAIRAMGLKDAAK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 ALM +GVPVVPGY G +QD + LA A IGYPVLIKA AGGGGKGMRRVE E F A Sbjct: 121 ALMAEAGVPVVPGYQGADQDPARLAAEAEAIGYPVLIKAVAGGGGKGMRRVEGPEGFAGA 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 LEAAR EA AFG+ VLLE+Y+ PRHIE+QVFGD VHLFERDCSLQRRHQKVIE Sbjct: 181 LEAARAEARGAFGNDHVLLEKYVATPRHIELQVFGD-GARAVHLFERDCSLQRRHQKVIE 239 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAPAPGMT E+R AMG AAVRAA+AIGY GAGTVEFI D ++GL PD F+FMEMNTRLQV Sbjct: 240 EAPAPGMTPEMRAAMGAAAVRAAEAIGYAGAGTVEFIVDASDGLRPDRFWFMEMNTRLQV 299 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EHPVTEA+TG+DLV WQLRVASGEPLP +Q D+S+ G AFEARLYAED +GFLPATGRL Sbjct: 300 EHPVTEAVTGVDLVAWQLRVASGEPLPARQEDLSLRGHAFEARLYAEDVPKGFLPATGRL 359 Query: 361 TELSFPEGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTV 420 T L+FP +R+++GVR GD I+P+YDP+IAKL+VHG R +AL +L L C + G+V Sbjct: 360 THLAFP-ADARIETGVRAGDEISPWYDPMIAKLVVHGPTRQSALRKLDRVLAGCEVAGSV 418 Query: 421 TNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEALALAAIFSTGALDPNRST 480 TN FL L F +G DTGLIDRE+E L+ P A ALAA+ + G + Sbjct: 419 TNLAFLRALARHGGFFAGEVDTGLIDREVETLSPAPVPCSRARALAALGAAGLHEGGPDG 478 Query: 481 DPWSSLGSWQIWGDAHRMVVIEHADVRATVTLASRGRDQFAVRAGASTLPVLVLDRFEGG 540 + +W + + + + +RG F V G +T + G Sbjct: 479 ------AGFTLWAPLVQAQGLRFGEAEIEARIETRGAGSFRVGIGEATHEIT-----RRG 527 Query: 541 ARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDELVAPMPGLVK 600 V G R +++F G N F PD L ++ + APMPGLVK Sbjct: 528 GAWWVDGAPTPARIVVHAAGVSVF-WGNNYHFTAPDPLHRAGAAGPGAGHVEAPMPGLVK 586 Query: 601 LVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEGTVLVTL 656 V V GD V +G L ++EAMKME TL+A R+G ++ V VAEGAQVS G L+ L Sbjct: 587 AVFVAPGDTVAQGARLAILEAMKMEHTLTAGRDGVVSEVLVAEGAQVSAGAPLILL 642 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: 1329 Number of extensions: 68 Number of successful extensions: 5 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: 662 Length of database: 661 Length adjustment: 38 Effective length of query: 624 Effective length of database: 623 Effective search space: 388752 Effective search space used: 388752 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: 54 (25.4 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