Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ac3H11_3016 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3016 Length = 675 Score = 626 bits (1615), Expect = 0.0 Identities = 352/670 (52%), Positives = 432/670 (64%), Gaps = 13/670 (1%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF K+LIANRGEIACR+ TA+RLG++TVAVYSDAD +A HVA+ DEA+ IGG+ +SY Sbjct: 1 MFKKILIANRGEIACRVAATAQRLGVKTVAVYSDADANAKHVAVCDEAVHIGGSAPKDSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L I++AA++ GAQAIHPGYGFLSEN DFA+A A AG++F+GPP +AI+ MGLK +K Sbjct: 61 LRWERIIEAAKATGAQAIHPGYGFLSENEDFAQACAAAGLVFIGPPASAIKDMGLKAESK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 LME++GVP+VPGYHG +QD + L A IGYPVLIKA AGGGGKGMR V++ EDF A Sbjct: 121 QLMEKAGVPLVPGYHGSDQDPALLQREADRIGYPVLIKASAGGGGKGMRAVDKSEDFAAA 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 LE+ +REA ++FGD +VL+E+Y+ +PRHIE+QVFGD HGN V+LFERDCS+QRRHQKV+E Sbjct: 181 LESCKREAINSFGDDAVLVEKYVQRPRHIEIQVFGDMHGNCVYLFERDCSVQRRHQKVLE 240 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGL-WPDH--FYFMEMNTR 297 EAPAPGMT +R MG+AAV AA+A+ YVGAGTVEFI + G PD FYFMEMNTR Sbjct: 241 EAPAPGMTPALRAQMGEAAVAAAKAVNYVGAGTVEFIVEQPGGYERPDQMKFYFMEMNTR 300 Query: 298 LQVEHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPAT 357 LQVEHPVTEAITG+DLVEWQLRVASGEPLP +Q D+ + G A EAR+ AE+P FLPAT Sbjct: 301 LQVEHPVTEAITGLDLVEWQLRVASGEPLPLQQQDLRITGHAIEARICAENPDNNFLPAT 360 Query: 358 GRLTELSFPE------GTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDAL 411 G L + PE G RVDSGVRQGD I+P+YD ++AKLIVHG R AL RL DAL Sbjct: 361 GALNVYALPECVTFERGAIRVDSGVRQGDAISPFYDSMVAKLIVHGDTREQALARLDDAL 420 Query: 412 KECRIGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEALALAAIFST 471 + I G TN FL R+ + F DT LI RE L G A AA+ T Sbjct: 421 AQTHIVGLATNVQFLRRVAKTDAFAQAKLDTALIPREQAVLFHQEPVGLPLAAAAAVAQT 480 Query: 472 GALD-PNRSTDPWSSLGSWQIWGDAHRMVVIEHA--DVRATVTLASRGRDQFAVRAGAST 528 + + DP+S + G R E +A +T G AV G + Sbjct: 481 LLKERASEGVDPFSRRDGFHTHGVVQRRFEFEFGGEHAKALLTYERGGSLHLAVGEGETA 540 Query: 529 LP-VLVLDRFEGGARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIA 587 + LV G L+ AGQ+ E +F D L Sbjct: 541 VAGPLVFAPQADGIELQFAGQRTRAAVYAQGEVDHVFTPLGATQITAIDLLAHAGEVAAE 600 Query: 588 DDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQV 647 L APMPG V V AGD V KGQ L VMEAMKME T++A +G + + A G QV Sbjct: 601 GGRLTAPMPGKVVSFAVKAGDTVAKGQPLAVMEAMKMEHTIAAPADGVVQELLYAPGDQV 660 Query: 648 SEGTVLVTLM 657 +EG L+ L+ Sbjct: 661 TEGAELLKLV 670 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: 1179 Number of extensions: 55 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 662 Length of database: 675 Length adjustment: 38 Effective length of query: 624 Effective length of database: 637 Effective search space: 397488 Effective search space used: 397488 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