Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011604307.1 FRAAL_RS13795 acetyl-CoA carboxylase subunit beta
Query= metacyc::MONOMER-17283 (535 letters) >NCBI__GCF_000058485.1:WP_011604307.1 Length = 560 Score = 705 bits (1819), Expect = 0.0 Identities = 350/532 (65%), Positives = 406/532 (76%) Query: 4 IHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTL 63 + S + SP + H +L A+LRERLA GG RRRH ERGKL R+RI+ L Sbjct: 29 LRSAVDAASPAARGYSETHTALVAELRERLAAAALGGPEPVRRRHVERGKLLARERIEVL 88 Query: 64 IDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVK 123 +DP S FLE+ LAA +YD + P AGIV GIGR+AGR +++ANDATVKGGTY+PLTVK Sbjct: 89 LDPGSPFLELSPLAADGMYDGDAPGAGIVTGIGRIAGRECVVVANDATVKGGTYYPLTVK 148 Query: 124 KHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIAC 183 KHLRAQE+A NRLPC+YLVDSGGA+LP+Q +VFPDR+HFGRIFYNQA MS GI QIA Sbjct: 149 KHLRAQEVALHNRLPCVYLVDSGGAFLPMQDDVFPDREHFGRIFYNQATMSKAGIAQIAA 208 Query: 184 VMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISG 243 V+GS TAGGAYVPAMSDE VIV+ GTIFLGGPPLVKAATGE V AE+LGG +H + SG Sbjct: 209 VLGSSTAGGAYVPAMSDETVIVRNQGTIFLGGPPLVKAATGEVVAAEDLGGGLLHAKTSG 268 Query: 244 VADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDV 303 V D+ A+DD +AL VR IVA+L PR W + E P DP +Y +P D R YDV Sbjct: 269 VVDHLADDDADALQTVRRIVANLAPRAARPWPVAAVEEPAVDPAGLYAAVPTDSRTPYDV 328 Query: 304 REVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELC 363 REVIARIVDGSR EFK YG+TLV G A + G PVGI+ANNG+LF ESALKGAHFIELC Sbjct: 329 REVIARIVDGSRFAEFKREYGSTLVTGTARLHGHPVGIVANNGVLFGESALKGAHFIELC 388 Query: 364 CARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYG 423 R IPLVFLQNI+GFMVG++YE GGIAK GAK+VTAV+CA VPKFTV+IGGSFGAGNY Sbjct: 389 DQRGIPLVFLQNISGFMVGREYEAGGIAKHGAKMVTAVACARVPKFTVVIGGSFGAGNYS 448 Query: 424 MCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILA 483 MCGRAY PR LWMWPNARISVMGG QAA VL T+RR+ ARGQD E +E F API Sbjct: 449 MCGRAYSPRFLWMWPNARISVMGGEQAAAVLATVRREQYAARGQDWPAEAEEDFRAPIRE 508 Query: 484 KYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535 +YE +G PYY++ARLWDDGVIDP +TR VL L L+ AA AP+ P +G+FRM Sbjct: 509 RYEVQGSPYYSTARLWDDGVIDPRDTRTVLGLALSVAANAPMDPPGYGIFRM 560 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: 1012 Number of extensions: 50 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: 560 Length adjustment: 36 Effective length of query: 499 Effective length of database: 524 Effective search space: 261476 Effective search space used: 261476 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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