Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_015799731.1 BMI_RS08045 propionyl-CoA synthetase
Query= reanno::Phaeo:GFF1175 (629 letters) >NCBI__GCF_000022745.1:WP_015799731.1 Length = 636 Score = 806 bits (2082), Expect = 0.0 Identities = 389/637 (61%), Positives = 480/637 (75%), Gaps = 14/637 (2%) Query: 2 SYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLY-EWFADARVNTCYNAVDR 60 +Y+E Y W+ +PE FW +AA AI W P + + G+G Y W+ A NTCYNA+DR Sbjct: 4 NYAETYAAWQNDPEGFWADAAAAIDWFK-PWEQVFAGGEGTYGRWYTGAECNTCYNALDR 62 Query: 61 HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120 HV GRG+Q A+IY+SPIT R+I+Y EL V LA + GV+KGDR++IYMP +P Sbjct: 63 HVANGRGDQLALIYESPITGKTRKITYHELLEEVEALAAVMLDNGVQKGDRILIYMPTVP 122 Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180 EA+ AMLA AR+GA+HSVVFGGFAANELA RIDDA P IIAASCG+EP R V Y+ +LD Sbjct: 123 EAVVAMLASARIGAIHSVVFGGFAANELATRIDDAKPVMIIAASCGIEPSRVVPYQAMLD 182 Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAE-----CVPVEGNHPAY 235 AI LA HK D C+IFQREQ +EGRD++ ++ V+ A CVPV P Y Sbjct: 183 KAISLAHHKVDHCIIFQREQHRHLPVEGRDID---YREAVDAARGRHVPCVPVAATDPLY 239 Query: 236 ILYTSGTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGP 295 +LYTSGTTG+PKGV+R G +VAL W+MK++++V PG V+WAASDVGWVVGHSYI Y P Sbjct: 240 VLYTSGTTGEPKGVVRDNGGHMVALVWSMKHVFDVKPGQVWWAASDVGWVVGHSYIVYAP 299 Query: 296 LIHGNTTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDL 355 L+ G T+I+FEGKP+GTPDAG +WR+I EH V+ FTAPTA RA+K+ED G FV+++DL Sbjct: 300 LLIGATSILFEGKPVGTPDAGEYWRIIEEHGVEVMFTAPTALRAIKKEDADGHFVRRHDL 359 Query: 356 SCLKQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPA 415 S + +YLAGERADP+TI WA+ L PVIDHWWQTE+GW + ANPLG+ L TK GSPA Sbjct: 360 SGFRALYLAGERADPETIHWAENLLGCPVIDHWWQTESGWPMVANPLGLGLLETKYGSPA 419 Query: 416 VPMPGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYE 475 V +PGY + +LD+ GH V PG LG I +KLPLPPG LPTLWNA++RF+K+YL FPGYY+ Sbjct: 420 VCLPGYDIRVLDDEGHEVEPGTLGNILIKLPLPPGCLPTLWNADERFRKAYLNEFPGYYK 479 Query: 476 TGDAGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQ 535 T DAG DEDGYLYIM+RTDD+INVAGHRLSTGAMEEVL+ HPDVAECAV+G+SD LKGQ Sbjct: 480 TADAGYMDEDGYLYIMSRTDDIINVAGHRLSTGAMEEVLSSHPDVAECAVLGISDPLKGQ 539 Query: 536 APVGFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMV 595 P GFL L + D ++V + + ++R+ IGPVAAF+LA V RLPKTRSGKILR T+ Sbjct: 540 VPCGFLVLKSNIDRDPQEVEKECISMIRDAIGPVAAFRLALAVKRLPKTRSGKILRSTIQ 599 Query: 596 NIADGTDWKMPATIDDPAILDEITTALQ----GLGYA 628 +ADG +WKMPATIDDPAILDEI T L+ GL +A Sbjct: 600 KMADGQEWKMPATIDDPAILDEIGTVLRERHIGLAFA 636 Lambda K H 0.318 0.137 0.428 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: 1406 Number of extensions: 53 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: 629 Length of database: 636 Length adjustment: 38 Effective length of query: 591 Effective length of database: 598 Effective search space: 353418 Effective search space used: 353418 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