Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate AZOBR_RS22285 AZOBR_RS22285 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__azobra:AZOBR_RS22285 Length = 667 Score = 690 bits (1781), Expect = 0.0 Identities = 372/662 (56%), Positives = 455/662 (68%), Gaps = 22/662 (3%) Query: 10 RLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRG 69 ++L+ANRGEIACRV+R+AR +GI +VAV+S+ D A HV AD AV +G A +SYLRG Sbjct: 4 KILIANRGEIACRVIRTARRMGIRTVAVYSEADARAMHVEMADEAVCIGPAPVGESYLRG 63 Query: 70 DRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALM 129 D I+ A +GAQAIHPGYGFLSENA FA AC EAG++F+GPP AI MGSK+ +K +M Sbjct: 64 DAILEVAKRTGAQAIHPGYGFLSENAGFAAACAEAGVVFIGPPIEAIRVMGSKAESKRVM 123 Query: 130 EEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSS 189 +A VPLVPG+HGEAQDLET EA RIGYPVL+KA+AGGGGKGM+VV E A+A++ Sbjct: 124 SQADVPLVPGFHGEAQDLETLSAEAERIGYPVLVKASAGGGGKGMRVVRAAGEFADAVAG 183 Query: 190 AQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAP 249 A+REAKAAFGD +L+EKYL +PRHVEIQVF D HG+ +YL ERDCSIQRRHQKV+EEAP Sbjct: 184 AKREAKAAFGDDSVLLEKYLGRPRHVEIQVFCDTHGNGVYLFERDCSIQRRHQKVIEEAP 243 Query: 250 APGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTEAI 309 AP L +LRR MGEAAV AA+A+ YVGAGTVEFL ++ G F+F+EMNTRLQVEHPVTE I Sbjct: 244 APALPDDLRRRMGEAAVAAAKAVNYVGAGTVEFLYED-GGFYFIEMNTRLQVEHPVTEKI 302 Query: 310 TGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAAA 369 TG DLV WQ+RVA G LPL Q+Q+ GHA E RLYAEDP+ +FLPA G+L+ R A Sbjct: 303 TGQDLVEWQLRVAAGGVLPLMQDQLTRRGHAFEARLYAEDPQREFLPAIGKLVRLRPPAE 362 Query: 370 GPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAFL 429 RVD+GVREGDEV+ FYDPM+AKLI W E R+ A +RL LA V G+ TN+AFL Sbjct: 363 NEHVRVDTGVREGDEVTMFYDPMIAKLIVWDEDRDAALRRLRVALAAYEVVGVTTNVAFL 422 Query: 430 RRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWL-----QSEPGHRRD 484 I GHPAF A E+DTGFI RH+ DLLP P +P+ AA + L + R Sbjct: 423 GAIAGHPAFRAVEIDTGFIERHRADLLPPPAPVPDRGLAIAALSVLLRRNADTRKARRAA 482 Query: 485 DDPHSPWSRNDGWRSALARESDLMLRCRDERRCVRLRHASPSQYR--------------- 529 DP SPW GWR DL L D R + L H P Y Sbjct: 483 SDPWSPWLSASGWRLNDDNHHDLRLMDGDTPRALTL-HFRPDGYEIEVEGRPAIRAERVT 541 Query: 530 LDGDDLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAPM 589 LDG+ L + +D V R+ + +G L + +G + + DP A A G L+APM Sbjct: 542 LDGETLTATIDAVRTRATVVCQGLDLTILSDGAVWRLHLDDPTARAAEQEGGSGRLTAPM 601 Query: 590 NGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLVE 649 G++VRVLVEPGQTVEAGA L++LEAMKMEH+I+AP AG V A+ + G+ V EG L+ Sbjct: 602 PGTVVRVLVEPGQTVEAGAPLMLLEAMKMEHTIKAPAAGTVSAVNFAAGDQVSEGVDLLV 661 Query: 650 LD 651 LD Sbjct: 662 LD 663 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: 1109 Number of extensions: 44 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: 667 Length adjustment: 38 Effective length of query: 617 Effective length of database: 629 Effective search space: 388093 Effective search space used: 388093 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