Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate RR42_RS26895 RR42_RS26895 3-methylcrotonyl-CoA carboxylase
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__Cup4G11:RR42_RS26895 Length = 674 Score = 677 bits (1746), Expect = 0.0 Identities = 367/668 (54%), Positives = 451/668 (67%), Gaps = 25/668 (3%) Query: 10 RLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRG 69 ++L+ANRGEIACRV + R LGI +VAV+SD D ARHVA D AV +GGA DSYLRG Sbjct: 4 KILIANRGEIACRVAATCRRLGIRTVAVYSDADADARHVALCDEAVHIGGAPARDSYLRG 63 Query: 70 DRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALM 129 D II A A+GAQAIHPGYGFLSEN FA AC EAGL+F+GPPA++I AMGSKSAAK LM Sbjct: 64 DHIIEMAKATGAQAIHPGYGFLSENDGFAEACAEAGLVFIGPPASSIRAMGSKSAAKRLM 123 Query: 130 EEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSS 189 E A VPLVPGYHGE Q+ RREA RIGYPVLLKA+AGGGGKGM+VVE AL+S Sbjct: 124 EAAAVPLVPGYHGEDQEPALLRREADRIGYPVLLKASAGGGGKGMRVVEASEGFEAALAS 183 Query: 190 AQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAP 249 QREA A+FGD R+LVEKYL +PRH+EIQVFAD HG+C+YL ERDCS+QRRHQKV+EEAP Sbjct: 184 VQREASASFGDDRVLVEKYLTRPRHIEIQVFADTHGNCVYLFERDCSVQRRHQKVLEEAP 243 Query: 250 APGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTEAI 309 APG+ E RRAMGEAAV AAQA+GYVGAGTVEF+ ++ G F+FMEMNTRLQVEHPVTE I Sbjct: 244 APGMSEERRRAMGEAAVAAAQAVGYVGAGTVEFIANQDGSFYFMEMNTRLQVEHPVTEMI 303 Query: 310 TGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAAA 369 TG DLV WQ+RVA GE LPL Q+Q+ ++GHA+E R+YAE+P+ FLP++G L R AA Sbjct: 304 TGQDLVEWQLRVAAGEPLPLRQDQLQIHGHALEARVYAENPDKGFLPSTGTLRYLRTPAA 363 Query: 370 ----------GP-GRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETS 418 GP G R+DSGVREGD +SP+YDPM+AKLI WG REEA R+ LAE Sbjct: 364 VTFALGQDGNGPAGVRIDSGVREGDTISPYYDPMIAKLIVWGRDREEALARMAQALAEYH 423 Query: 419 VGGLRTNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQSE 478 V GL TN+AFL+R++ AF A+LDTG I R+Q L P P + A A + ++ Sbjct: 424 VVGLSTNIAFLQRLVTSQAFRTADLDTGLIERNQAALFPPPAKVGTEVIALAVAALVDAD 483 Query: 479 PGHRRDD--DPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYRLDGDD-L 535 RR D D HSPW WR S LR + LR Q+ G+ L Sbjct: 484 TRARRVDPADAHSPWQNAGAWRLNADATSQFRLRTGEGETLASLRSDGGKQWLTVGEQTL 543 Query: 536 VSRVDGV-----------TRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGG 584 RV + T + + G L++ + +E +DP+A A +A A G Sbjct: 544 PLRVTSLAGSHALDLGERTVKGSTYIEGDALYVFSGKQQTRLEVIDPLAHAGSADAEGGK 603 Query: 585 LSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEG 644 L APM G I+ V+V+ G + G L+V+EAMKMEH++ AP GVV+ + G+ V++G Sbjct: 604 LVAPMPGRIIAVMVKAGTVIGKGDPLIVMEAMKMEHTLTAPADGVVQEVLYGIGDQVQDG 663 Query: 645 TPLVELDE 652 LV L++ Sbjct: 664 AQLVTLED 671 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: 1113 Number of extensions: 45 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: 655 Length of database: 674 Length adjustment: 38 Effective length of query: 617 Effective length of database: 636 Effective search space: 392412 Effective search space used: 392412 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