Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate HSERO_RS23460 HSERO_RS23460 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__HerbieS:HSERO_RS23460 Length = 671 Score = 684 bits (1766), Expect = 0.0 Identities = 370/667 (55%), Positives = 458/667 (68%), Gaps = 30/667 (4%) Query: 10 RLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRG 69 ++L+ANRGEIACRV +AR LGI +VAV+SD D A+HVA D +V LG A +SYL Sbjct: 4 KILIANRGEIACRVAATARRLGIATVAVYSDADARAKHVAACDESVRLGPAPARESYLCA 63 Query: 70 DRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALM 129 ++IIAAALA+GAQAIHPGYGFLSENA FA+AC +AGL+F+GPPA+AI+AMGSK+AAKALM Sbjct: 64 EKIIAAALATGAQAIHPGYGFLSENAGFAQACAQAGLVFIGPPASAIEAMGSKAAAKALM 123 Query: 130 EEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSS 189 E+A VPLVPGYHGE Q+ +A RIGYPVLLKA+AGGGGKGM+VVER + AL+S Sbjct: 124 EQAAVPLVPGYHGEEQESGLLHSQADRIGYPVLLKASAGGGGKGMRVVERSEDFDAALAS 183 Query: 190 AQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAP 249 +REA A+FGD R+LVEKYL +PRH+EIQVFAD HGHC+YL ERDCS+QRRHQKV+EEAP Sbjct: 184 CKREAIASFGDDRVLVEKYLTRPRHIEIQVFADGHGHCVYLFERDCSVQRRHQKVLEEAP 243 Query: 250 APGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTEAI 309 APG+ E R AMGEAAV AA+A+GYVGAGTVEF+ ++ G F+FMEMNTRLQVEHPVTE I Sbjct: 244 APGMSEERRAAMGEAAVAAARAVGYVGAGTVEFIANQDGSFYFMEMNTRLQVEHPVTEMI 303 Query: 310 TGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAAA 369 TGLDLV WQ+RVA G+ALPL QEQ+ ++GHAIE R+YAE+PE FLPA G L R AAA Sbjct: 304 TGLDLVEWQLRVAAGQALPLKQEQLRIHGHAIEARIYAENPEKGFLPAIGTLTRMRSAAA 363 Query: 370 --------GPGR----RVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAET 417 PG R+D+GVREGD +SPFYDPM+AKLI WG R+ A + + LA+ Sbjct: 364 VEFRLGQSAPGDPAHVRIDAGVREGDAISPFYDPMIAKLIVWGPDRDAALRNMQRALAQY 423 Query: 418 SVGGLRTNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWLQS 477 V GL TN+AFL+R++ AF+ A LDTG I RH+D L P P + A A LQ Sbjct: 424 QVVGLATNIAFLQRLVAGQAFSTAALDTGLIERHRDTLFPPPSSPDTETLALAIAAILQQ 483 Query: 478 EPGHRRDDDPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQ---------- 527 E D PWS+ +GWR L V+L +A Q Sbjct: 484 EHAQAERSD---PWSQRNGWRLNTRLLRTLRFEHDAGDTTVQLDYAGDGQHWSLLTNGQT 540 Query: 528 -----YRLDGDDLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQ 582 + DGD L+ +DG T R+ LR G L + ++ VDP+A A + A Sbjct: 541 HALQLHAADGDTLIISLDGRTLRADVLREGEWLHVFDAHGQHSLRHVDPLAHAGHSEAEG 600 Query: 583 GGLSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVE 642 G L+APM G IV +LV+ G +V G L+++EAMKMEH+I AP GVV+ L + G+ V Sbjct: 601 GRLTAPMPGKIVALLVQKGASVAHGTPLLIMEAMKMEHTIAAPADGVVEDLLYAVGDQVA 660 Query: 643 EGTPLVE 649 EG L+E Sbjct: 661 EGAQLLE 667 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: 1135 Number of extensions: 54 Number of successful extensions: 7 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: 655 Length of database: 671 Length adjustment: 38 Effective length of query: 617 Effective length of database: 633 Effective search space: 390561 Effective search space used: 390561 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