Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate HSERO_RS23455 HSERO_RS23455 methylcrotonoyl-CoA carboxylase
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__HerbieS:HSERO_RS23455 Length = 544 Score = 740 bits (1910), Expect = 0.0 Identities = 368/544 (67%), Positives = 423/544 (77%), Gaps = 9/544 (1%) Query: 1 MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60 M I S + P S DFQ N A Q + DLRE++A I +GGG R +H RGKL RDR+ Sbjct: 1 MPQIESKLNPRSEDFQNNRAAMQRIVDDLREKIAAIAEGGGQAAREKHLARGKLLPRDRV 60 Query: 61 DTLIDPDSSFLEIGALAAYNVYDEE---------VPAAGIVCGIGRVAGRPVMIIANDAT 111 L+DP + FLE LAAY +Y E+ P+AGI+ GIGRVAG+ +I+ NDAT Sbjct: 61 QMLLDPGTPFLEFSQLAAYGMYREKDRDGQPKDAAPSAGIITGIGRVAGQECVIVCNDAT 120 Query: 112 VKGGTYFPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQA 171 VKGGTY+P+T KKHLRAQEIA N LPCIYLVDSGGA LP Q EVFPDRDHFGRIFYNQA Sbjct: 121 VKGGTYYPMTAKKHLRAQEIAEFNHLPCIYLVDSGGANLPNQDEVFPDRDHFGRIFYNQA 180 Query: 172 QMSAEGIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEE 231 +SA+GI QIA VMGSCTAGGAYVPAMSDE +IVK TIFL GPPLVKAATGE V+AEE Sbjct: 181 NLSAKGIAQIAVVMGSCTAGGAYVPAMSDESIIVKDQATIFLAGPPLVKAATGEVVSAEE 240 Query: 232 LGGADVHTRISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYG 291 LGG DVHTR+SGVAD+ A DD ALAI R+IV HL R+ LR+ PRY +E+YG Sbjct: 241 LGGGDVHTRLSGVADHLAQDDTHALAIARNIVGHLNRRKPQPLALRESIEPRYPAQELYG 300 Query: 292 ILPRDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSE 351 ++P D R+ +DVREVIARIVD S EFK RYGTTLVCGFAH+ G PVGI+ANNGILFSE Sbjct: 301 VIPTDTRKPFDVREVIARIVDASEFDEFKARYGTTLVCGFAHLHGMPVGIIANNGILFSE 360 Query: 352 SALKGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTV 411 +A KG HFIELCC R IPL+FLQNITGFMVGK+YEN GIA+ GAK+VTAVS A VPK TV Sbjct: 361 AAEKGTHFIELCCQRKIPLIFLQNITGFMVGKKYENEGIARHGAKMVTAVSTAKVPKLTV 420 Query: 412 IIGGSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTP 471 IIGGSFGAGNYGMCGRA+ PR LWMWPNARISVMGG QAA+VL T++RD + ARG + Sbjct: 421 IIGGSFGAGNYGMCGRAFSPRFLWMWPNARISVMGGEQAASVLATVKRDGIEARGGSWSA 480 Query: 472 EEQERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFG 531 EE+ F PI A+YE +GHPYYASARLWDDGVIDP +TR+VLALGL+AA AP++ TRFG Sbjct: 481 EEEAAFKEPIRAQYETQGHPYYASARLWDDGVIDPADTRQVLALGLSAALNAPIEETRFG 540 Query: 532 VFRM 535 VFR+ Sbjct: 541 VFRI 544 Lambda K H 0.322 0.139 0.423 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: 979 Number of extensions: 43 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: 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 (21.9 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