Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_084199287.1 C0029_RS09450 propionyl-CoA synthetase
Query= BRENDA::A0A0G2K047 (683 letters) >NCBI__GCF_002869505.1:WP_084199287.1 Length = 618 Score = 692 bits (1785), Expect = 0.0 Identities = 320/608 (52%), Positives = 440/608 (72%), Gaps = 2/608 (0%) Query: 73 WGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGDKIAIIYDSP 132 W +AA+ + W+K + L++ PP WF +G N CYNA+D H+ G+G++ A+IYDSP Sbjct: 7 WREAAQAVHWFKTPQQVLDDSEPPFYRWFPDGQTNACYNALDVHVAEGRGEQTALIYDSP 66 Query: 133 VTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLACARIGAIHS 192 VTDT +Y ++L+QV++ AGVL GV +GD V++YMPM+P+A+ AMLACAR+GA+HS Sbjct: 67 VTDTCRRYTYTQLLDQVARFAGVLADHGVGRGDRVIVYMPMVPEALIAMLACARLGAVHS 126 Query: 193 LIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQHKPDRLLIYN 252 ++FGGFAS EL+ RID PK++V+AS G+EP R V Y PLL+ A+ + QHKPD +I Sbjct: 127 VVFGGFASNELAVRIDDATPKLIVSASCGVEPNRIVAYKPLLDAAIELAQHKPDNCVILQ 186 Query: 253 RPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVVRPTGGY 312 RP M+ L++GRD+DW + MA A++ C PV + PLY+LYTSGTTG PKGVVR TGG Sbjct: 187 RP-MQPAELIAGRDVDWTQAMADARAVPCTPVAANDPLYVLYTSGTTGQPKGVVRDTGGS 245 Query: 313 AVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPVGTPDAG 372 V L W+M +IY ++PG+V+WAASD+GWVVGHSYI YGPL G TV+YEGKPVGTPD G Sbjct: 246 IVALKWSMKAIYDVEPGDVYWAASDVGWVVGHSYIVYGPLFSGCATVIYEGKPVGTPDPG 305 Query: 373 AYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERCDVETLEWS 432 A++RV+ ++ V LFTAPTA RAI+++DP +QY+++ ++LF+AGERCD TL W+ Sbjct: 306 AFWRVIEDYQVKVLFTAPTAFRAIKKEDPAGKYLQQYNVSSLRSLFLAGERCDPSTLAWA 365 Query: 433 KKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPGYNVMILDDNMQKLKA 492 ++ +VPV+DHWWQTETG PI A+C+G+ + PG + VPGY V +LD N +++ A Sbjct: 366 QQQLKVPVIDHWWQTETGWPICANCLGI-EALPIVPGSPARPVPGYYVQVLDGNGEQVSA 424 Query: 493 RSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEGYLYVMSRVD 552 +G +VVK PLPPG F+ LW+ +E ++ YF ++PGYY+T DAGY+D GY++VM+R D Sbjct: 425 GEIGALVVKSPLPPGTFTTLWQAEERYQSAYFARYPGYYETGDAGYIDANGYVFVMARTD 484 Query: 553 DVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLKKDVNATEEQVL 612 DVINVAGHR+S GA+EE + H V +CAVVG DP+KG +PL L VL V+ Sbjct: 485 DVINVAGHRLSTGAMEEVLAEHPDVAECAVVGVADPMKGQLPLGLLVLNAGAERATADVV 544 Query: 613 EEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYKVTPTIEDPSIF 672 E ++ VR IGPVAAF+ V++LPKTRSGKI R T+ ++ +G+P+K+ TI+DP I Sbjct: 545 RESLQLVRDKIGPVAAFKLCTVVERLPKTRSGKILRGTMRSIADGEPWKMPATIDDPVIL 604 Query: 673 GHIEEVLK 680 I E L+ Sbjct: 605 DEITEALR 612 Lambda K H 0.318 0.136 0.421 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: 1316 Number of extensions: 72 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: 683 Length of database: 618 Length adjustment: 38 Effective length of query: 645 Effective length of database: 580 Effective search space: 374100 Effective search space used: 374100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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