Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate HSERO_RS23455 HSERO_RS23455 methylcrotonoyl-CoA carboxylase
Query= reanno::SB2B:6937191 (535 letters) >FitnessBrowser__HerbieS:HSERO_RS23455 Length = 544 Score = 809 bits (2089), Expect = 0.0 Identities = 395/544 (72%), Positives = 455/544 (83%), Gaps = 9/544 (1%) Query: 1 MTQLTSRVNPRSDEFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARV 60 M Q+ S++NPRS++F+ AM +V DL++K+A I +GGG A E+HL+RGKL PR RV Sbjct: 1 MPQIESKLNPRSEDFQNNRAAMQRIVDDLREKIAAIAEGGGQAAREKHLARGKLLPRDRV 60 Query: 61 EKLLDPGSPFLELSQFAAFEVYDED---------VPAAGIIAGIGRVSGVECMIIANDAT 111 + LLDPG+PFLE SQ AA+ +Y E P+AGII GIGRV+G EC+I+ NDAT Sbjct: 61 QMLLDPGTPFLEFSQLAAYGMYREKDRDGQPKDAAPSAGIITGIGRVAGQECVIVCNDAT 120 Query: 112 VKGGTYYPITVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQA 171 VKGGTYYP+T KKHLRAQ IAE HLPCIYLVDSGGANLP QDEVFPDRDHFGRIF+NQA Sbjct: 121 VKGGTYYPMTAKKHLRAQEIAEFNHLPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQA 180 Query: 172 RMSAKGIPQIAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEE 231 +SAKGI QIAVVMG CTAGGAYVPAM+DESIIV++Q TIFLAGPPLVKAATGE VSAEE Sbjct: 181 NLSAKGIAQIAVVMGSCTAGGAYVPAMSDESIIVKDQATIFLAGPPLVKAATGEVVSAEE 240 Query: 232 LGGGDVHTKISGVADHLAQNDEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYG 291 LGGGDVHT++SGVADHLAQ+D HAL +AR V LN +K L L + P+Y ELYG Sbjct: 241 LGGGDVHTRLSGVADHLAQDDTHALAIARNIVGHLNRRKPQPLALRESIEPRYPAQELYG 300 Query: 292 IVGTDLKKPFDVKEVIARIVDDSDFDEFKANYGTTLVCGFARIHGYPVGIVANNGILFSE 351 ++ TD +KPFDV+EVIARIVD S+FDEFKA YGTTLVCGFA +HG PVGI+ANNGILFSE Sbjct: 301 VIPTDTRKPFDVREVIARIVDASEFDEFKARYGTTLVCGFAHLHGMPVGIIANNGILFSE 360 Query: 352 SAQKGAHFIELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTV 411 +A+KG HFIELCCQRKIPL+FLQNITGFMVGKKYE+EGIA+HGAKMVTAVS A VPK TV Sbjct: 361 AAEKGTHFIELCCQRKIPLIFLQNITGFMVGKKYENEGIARHGAKMVTAVSTAKVPKLTV 420 Query: 412 LIGGSYGAGNYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSA 471 +IGGS+GAGNYGMCGRAF P +WMWPNARISVMGGEQAA VLATV++DG+ +G + SA Sbjct: 421 IIGGSFGAGNYGMCGRAFSPRFLWMWPNARISVMGGEQAASVLATVKRDGIEARGGSWSA 480 Query: 472 EEEAKFKAPIIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFG 531 EEEA FK PI AQY+ +GHPY+ASARLWDDG+IDPA TR VL L +SAALNAPIEETRFG Sbjct: 481 EEEAAFKEPIRAQYETQGHPYYASARLWDDGVIDPADTRQVLALGLSAALNAPIEETRFG 540 Query: 532 VFRM 535 VFR+ Sbjct: 541 VFRI 544 Lambda K H 0.320 0.137 0.405 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: 1009 Number of extensions: 42 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: 544 Length adjustment: 35 Effective length of query: 500 Effective length of database: 509 Effective search space: 254500 Effective search space used: 254500 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