Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate AZOBR_RS22295 AZOBR_RS22295 methylcrotonoyl-CoA carboxylase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2192 (535 letters) >FitnessBrowser__azobra:AZOBR_RS22295 Length = 535 Score = 815 bits (2105), Expect = 0.0 Identities = 397/535 (74%), Positives = 452/535 (84%) Query: 1 MATLHTQLNPRSPEFIANRDAMLGHVEALRTLLAQIRQGGGPKAQERHTSRGKLLPRERI 60 M L + LNPRS EF N DAM V LR + I+QGGG KA+++H SRGKLLPRERI Sbjct: 1 MTVLKSALNPRSAEFQTNADAMSTLVADLREKVGAIKQGGGAKARDKHLSRGKLLPRERI 60 Query: 61 NRLLDPGSPFLEISPLAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120 +LLD GSPFLE+S +AA++VY +D+PAAG+I GIG V G ECM+V NDATVKGG+Y+PL Sbjct: 61 RQLLDVGSPFLELSQMAAYKVYDDDIPAAGIITGIGSVAGQECMVVVNDATVKGGTYFPL 120 Query: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180 TVKKHLRAQ +AQQN LPCIYLVDSGGANLP QDEVFPDR+HFGRIFFNQANMSAQGIPQ Sbjct: 121 TVKKHLRAQEVAQQNNLPCIYLVDSGGANLPNQDEVFPDRDHFGRIFFNQANMSAQGIPQ 180 Query: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240 IAVVMGSCTAGGAYVPAM+DEAI+VR Q TIFL GPPLVKAATGEVVSAEDLGGADVH + Sbjct: 181 IAVVMGSCTAGGAYVPAMSDEAIIVRNQGTIFLGGPPLVKAATGEVVSAEDLGGADVHSR 240 Query: 241 ISGVADHYADSDEHALALARRSVANLNWRKQGELQHRLPIAPLYSGEELYGVVSADAKQP 300 SGV DHYA +D HALA+AR+ V+NLN K+ ++ R P P Y ELYGV+ +D ++P Sbjct: 241 TSGVTDHYAMNDAHALAMARKVVSNLNRSKRIDMDLREPQEPAYDPRELYGVIPSDPRKP 300 Query: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360 FDVREVIAR+VDGSV DEFK L+GTTLVCGFAH+ GYP+ I+ANNGILF+E+A KGAHF+ Sbjct: 301 FDVREVIARVVDGSVLDEFKPLYGTTLVCGFAHIFGYPVGIIANNGILFSESALKGAHFV 360 Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420 EL CQRGIPL+FLQNITGFMVG+KYEAGGIAK GAKLVTAVACAKVPKFTVIIGGS+GAG Sbjct: 361 ELCCQRGIPLVFLQNITGFMVGRKYEAGGIAKDGAKLVTAVACAKVPKFTVIIGGSYGAG 420 Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP 480 NYGMCGRAY PRFLWMWPN+RI VMG EQAAGVL QV+R+ E G ++ E+E K P Sbjct: 421 NYGMCGRAYSPRFLWMWPNSRISVMGGEQAAGVLAQVRRDAMESQGRSWAPEEEEAFKAP 480 Query: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM 535 I QYE+QGHPYY+SARLWDDG+IDPA TR VLGL LSASLNAP+E + FGVFRM Sbjct: 481 IRQQYEDQGHPYYASARLWDDGIIDPADTRMVLGLGLSASLNAPVEKTTFGVFRM 535 Lambda K H 0.321 0.137 0.411 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: 1036 Number of extensions: 40 Number of successful extensions: 1 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: 535 Length of database: 535 Length adjustment: 35 Effective length of query: 500 Effective length of database: 500 Effective search space: 250000 Effective search space used: 250000 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: 52 (24.6 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