Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CCNA_02252 CCNA_02252 methylcrotonyl-CoA carboxylase carboxyl transferase subunit
Query= reanno::Smeli:SM_b21122 (535 letters) >FitnessBrowser__Caulo:CCNA_02252 Length = 530 Score = 737 bits (1903), Expect = 0.0 Identities = 361/535 (67%), Positives = 431/535 (80%), Gaps = 5/535 (0%) Query: 1 MTVLRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRL 60 M L S I SS+ F N A + + V AA GG E+ARERH +RGKLLPR+R+ Sbjct: 1 MPKLNSVIDASSDAFAKNAAHNRALVDELRAKVAQAALGGPESARERHTARGKLLPRERV 60 Query: 61 ATLIDPGTPFLEVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPL 120 L+DPG+PFLEVG AA +YN +APGAG+I G+GR+S RE MIV NDPTVKGG Y+P+ Sbjct: 61 ERLLDPGSPFLEVGQLAACDLYNGEAPGAGMICGVGRVSGREVMIVANDPTVKGGAYFPM 120 Query: 121 TVKKHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQ 180 TVKKHLRAQEIAA+NRLPC+YLVDSGGANLP+Q EVFPDRDHFGRIF+NQA MSAA IPQ Sbjct: 121 TVKKHLRAQEIAAQNRLPCLYLVDSGGANLPHQAEVFPDRDHFGRIFFNQARMSAASIPQ 180 Query: 181 IAVVMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTR 240 IA VMGSCTAGGAYVPAMSDE +IV QGTIFLAGPPLV+AATGEV+SAE+LGGA+ H R Sbjct: 181 IACVMGSCTAGGAYVPAMSDETVIVRNQGTIFLAGPPLVKAATGEVISAEELGGAETHGR 240 Query: 241 LSGVADHLARDDAHALALARRAVSALNREKPWTVERIEPEPPLYDPEEIAGIVPADLKTP 300 SGV DH+A +D HAL + R V+ LN KP + +PEPP YDPEE+ GIVP D++ P Sbjct: 241 RSGVVDHVAENDEHALEIVRSIVANLNTTKPDQLVLADPEPPAYDPEELYGIVPTDVRAP 300 Query: 301 YEIREVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFV 360 Y++REVIAR+VDGS+FDEFKA +GTTLVCGFA + G PV I+ANNGVLFSESA+KGAHF+ Sbjct: 301 YDVREVIARIVDGSQFDEFKALYGTTLVCGFARIWGQPVAILANNGVLFSESALKGAHFI 360 Query: 361 ELCAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAG 420 EL +R+IPL+FLQNI+GFMVG KYE GIAK GAKLVTAVA+ +VPK T+L+GGSFGAG Sbjct: 361 ELACKRKIPLIFLQNISGFMVGGKYEAGGIAKDGAKLVTAVASAEVPKFTVLIGGSFGAG 420 Query: 421 NYGMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQP 480 NYGMCGRA+SPRFL+TWPNSRISVMGGEQAA VL++V +A K WS EE F+ P Sbjct: 421 NYGMCGRAYSPRFLFTWPNSRISVMGGEQAASVLATVHRDAAK-----WSPEEAEAFKAP 475 Query: 481 VLDLFERQSHPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLFRM 535 + +E + +P +A+ARLWDDG+IDP ++RD L L++SA+LNAPI ET FG+FRM Sbjct: 476 IRQRYEDEGNPYHATARLWDDGIIDPAQTRDALGLAISASLNAPIPETTFGVFRM 530 Lambda K H 0.320 0.136 0.404 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: 893 Number of extensions: 34 Number of successful extensions: 3 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: 530 Length adjustment: 35 Effective length of query: 500 Effective length of database: 495 Effective search space: 247500 Effective search space used: 247500 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