Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Dsui_0980 Dsui_0980 acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2192 (535 letters) >FitnessBrowser__PS:Dsui_0980 Length = 535 Score = 811 bits (2096), Expect = 0.0 Identities = 394/535 (73%), Positives = 455/535 (85%) Query: 1 MATLHTQLNPRSPEFIANRDAMLGHVEALRTLLAQIRQGGGPKAQERHTSRGKLLPRERI 60 M L TQLNPRS +F N DAM G V LR +A+I GG A+++H +RGKLLPRER+ Sbjct: 1 MTILKTQLNPRSEDFQHNADAMAGLVADLRQQMARIALGGPEAARQKHIARGKLLPRERV 60 Query: 61 NRLLDPGSPFLEISPLAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120 + LLDPG+PFLEI LAAH +YG DVPAA VIAGIGRV GVECMIVANDATVKGG+YYP+ Sbjct: 61 SALLDPGTPFLEIGQLAAHGMYGGDVPAASVIAGIGRVNGVECMIVANDATVKGGTYYPM 120 Query: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180 TVKKHLRAQ IA +NRLPCIYLVDSGGA LP QDEVFPD+EHFGRIFFNQAN+SAQGIPQ Sbjct: 121 TVKKHLRAQEIALENRLPCIYLVDSGGAFLPMQDEVFPDKEHFGRIFFNQANLSAQGIPQ 180 Query: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240 IA VMGSCTAGGAYVPAM+DE+I+V++Q TIFL GPPLVKAATGEVV+AEDLGGADVH + Sbjct: 181 IAAVMGSCTAGGAYVPAMSDESIIVKEQGTIFLGGPPLVKAATGEVVTAEDLGGADVHTR 240 Query: 241 ISGVADHYADSDEHALALARRSVANLNWRKQGELQHRLPIAPLYSGEELYGVVSADAKQP 300 +SGVADHYA++D+HALA+ARR V NLNW+KQ + P+ PLY+ EELYGV+ D K+P Sbjct: 241 VSGVADHYAENDQHALAIARRIVKNLNWQKQPSVSLSEPVEPLYAAEELYGVIPTDTKKP 300 Query: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360 FDVRE+IAR+VDGS FDEFKA +GTT+VCGFA + GYP+ I+ANNGILF+E+A K AHFI Sbjct: 301 FDVREIIARIVDGSDFDEFKARYGTTIVCGFARIWGYPVGIVANNGILFSESALKAAHFI 360 Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420 EL QR IPL+FLQNITGFMVG+KYE GGIA+ GAK+VTAVA AKVPKFTV+IGGSFGAG Sbjct: 361 ELCAQRNIPLVFLQNITGFMVGRKYENGGIARDGAKMVTAVATAKVPKFTVVIGGSFGAG 420 Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP 480 NYGMCGRAY PRFLWMWPNARI VMG EQA+ VL VKR+ E +G +SAE+E E ++P Sbjct: 421 NYGMCGRAYSPRFLWMWPNARISVMGGEQASSVLATVKRDGLEAAGKQWSAEEEEEFRRP 480 Query: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM 535 I +QYE QGHPYY+SARLWDDG+IDPA TR VLGL LSA++NAP E +RFGVFRM Sbjct: 481 IREQYETQGHPYYASARLWDDGIIDPADTRRVLGLGLSAAMNAPAEETRFGVFRM 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: 1004 Number of extensions: 41 Number of successful extensions: 2 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