Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011840850.1 RSPH17029_RS05950 biotin/lipoyl-binding protein
Query= reanno::Smeli:SM_b21124 (662 letters) >NCBI__GCF_000015985.1:WP_011840850.1 Length = 646 Score = 672 bits (1735), Expect = 0.0 Identities = 370/658 (56%), Positives = 453/658 (68%), Gaps = 15/658 (2%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF K+LIANRGEIA RI TARRLG+ TVAV+SDAD +ALHVA+ADEA+ IGG A+SY Sbjct: 1 MFRKILIANRGEIAVRIAATARRLGVATVAVHSDADAEALHVAVADEAVPIGGPQPADSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L +++AA + GA+AIHPGYGFLSEN +F EAV AG++F+GP AAIRAMGLKDAAK Sbjct: 61 LRGERLIEAALATGAEAIHPGYGFLSENPEFVEAVEAAGLVFIGPSAAAIRAMGLKDAAK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 ALM +GVPVVPGYHG +Q+ LA A++IGYPVLIKA AGGGGKGMRRVER E+F A Sbjct: 121 ALMAEAGVPVVPGYHGADQEPEHLALMAQDIGYPVLIKAVAGGGGKGMRRVERAEEFAAA 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 L +AR EA +AFG+ +VL+E+++ PRHIE+QVFGD + VHL+ERDCSLQRRHQKVIE Sbjct: 181 LASARAEARTAFGNEAVLIEKWIDCPRHIELQVFGD-GTDAVHLYERDCSLQRRHQKVIE 239 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAPAPGMT +R AMG+AAVRAA+AIGY GAGTVEFI D + GL PD F+FMEMNTRLQV Sbjct: 240 EAPAPGMTPGMRAAMGEAAVRAARAIGYRGAGTVEFIVDGSAGLSPDRFWFMEMNTRLQV 299 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EHPVTEA+TGIDLVEWQLRVA+GEPLP Q DI + G AFEARLYAED GFLPATGRL Sbjct: 300 EHPVTEAVTGIDLVEWQLRVAAGEPLPLAQKDIPLRGHAFEARLYAEDVPAGFLPATGRL 359 Query: 361 TELSFPEGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTV 420 L F +G R D+GVR GD I+P+YDP+IAK++ HG +R++AL RL AL+E + GTV Sbjct: 360 DHLRFADGI-RADTGVRTGDRISPWYDPMIAKIVAHGPSRASALNRLARALEETEVAGTV 418 Query: 421 TNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEALALAAIFSTGALDPNRST 480 TN FL RL + F +G DTGLI R++ L AP E +A A + + P Sbjct: 419 TNLAFLCRLAQHPGFAAGEVDTGLIGRDLAPLIAPATLAPETVAAALLVAELGETP---- 474 Query: 481 DPWSSLGSWQIWGDAHRMVVIEHADVRATVTLASRGRDQFAVRAGASTLPVLVLDRFEGG 540 + L + +W R V + H + L + V G + L + R EG Sbjct: 475 ---APLQGFSLWAPLRRHVRLRHGSEKIAAALTVEAPGRATVELGEARLAARL--RPEGW 529 Query: 541 ARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDELVAPMPGLVK 600 A +E R++R + +F + F +PD L G ++PMPGLV+ Sbjct: 530 A-VEGRPPARVLRIGAQ---VHVFARTGTVSFEIPDPLDRGTEEAGQGGLTLSPMPGLVR 585 Query: 601 LVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEGTVLVTLME 658 V V AGD V KG L V+EAMKME L+A+R+GT+A V V GAQV G LV L E Sbjct: 586 EVSVRAGDRVEKGDRLAVIEAMKMEHVLTAARDGTVAEVLVEAGAQVEAGAALVRLEE 643 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: 1250 Number of extensions: 48 Number of successful extensions: 4 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: 646 Length adjustment: 38 Effective length of query: 624 Effective length of database: 608 Effective search space: 379392 Effective search space used: 379392 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 Apr 10 2024. 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