Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_086509797.1 BZY95_RS10010 propionyl-CoA synthetase
Query= reanno::Phaeo:GFF1175 (629 letters) >NCBI__GCF_002151265.1:WP_086509797.1 Length = 636 Score = 756 bits (1952), Expect = 0.0 Identities = 361/622 (58%), Positives = 457/622 (73%), Gaps = 1/622 (0%) Query: 2 SYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRH 61 +Y ++ P+ FW + A I W + P L G W+ D +N C+ A+D H Sbjct: 3 AYKNEFQRSIEQPQSFWADQARRIPWFTPPKTILEYDEQGHARWYTDGELNLCHAALDHH 62 Query: 62 VEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPE 121 V+QGRG+Q AI +DSP+T KR ++Y E+R+ VA AGAL GVEKGDRV+IYMPM+PE Sbjct: 63 VDQGRGDQPAIYWDSPVTGGKRTLTYREMRDEVALFAGALEGLGVEKGDRVVIYMPMVPE 122 Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDG 181 AL AM ACARLGAVHSVVFGGFA +ELAVRIDDA PK ++AASCG+E R + Y+P + Sbjct: 123 ALVAMYACARLGAVHSVVFGGFAPHELAVRIDDAKPKVVVAASCGVEIDRVIAYQPNIAA 182 Query: 182 AIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSG 241 AI+L+ HKPD C+ QR+Q++AEL RD++W EPA+CVPV+G+ P Y+LYTSG Sbjct: 183 AIELSEHKPDACIYLQRQQQLAEL-GPRDLDWSELLESAEPADCVPVKGSDPLYVLYTSG 241 Query: 242 TTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNT 301 TTG+PKGV+R TAG VAL+++M+ IY+V PGDVF++ASDVGWVVGHSYI Y PL+ G T Sbjct: 242 TTGKPKGVVRDTAGYAVALHYSMETIYDVAPGDVFFSASDVGWVVGHSYIVYAPLLRGCT 301 Query: 302 TIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQV 361 T+V+EGKP+ TPDAG FWR+IS+++VKSFFTAPTAFRA+K+EDP G +++YD+SCLK + Sbjct: 302 TVVYEGKPVKTPDAGAFWRLISQYRVKSFFTAPTAFRAIKKEDPDGILLQQYDISCLKAL 361 Query: 362 YLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGY 421 YLAGER DP T W + L VPVIDHWWQTETGW IAAN G+E +PTK GS VP+PG+ Sbjct: 362 YLAGERLDPPTFHWLDDLLDVPVIDHWWQTETGWPIAANLQGLEPMPTKAGSATVPVPGF 421 Query: 422 TVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGM 481 V IL+ G AP E G++ +K P+PPG L +W RF +Y+ FPGYY TGD G Sbjct: 422 NVQILNREGEQAAPMEQGSVVIKQPMPPGCLIGVWGDPQRFHSAYMAAFPGYYLTGDGGY 481 Query: 482 KDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFL 541 DE GYL+IM RTDDVINVAGHRLSTG MEEV+ H VAECAVIG+ D+LKGQ PVG + Sbjct: 482 FDEQGYLFIMGRTDDVINVAGHRLSTGEMEEVVGAHRAVAECAVIGIHDALKGQIPVGLV 541 Query: 542 CLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGT 601 G D + +++ LVREKIGP+A FK VV+RLPKTRSGKILR + NIADG Sbjct: 542 IPKDGFDGDEVALENELIALVREKIGPIACFKQVLVVNRLPKTRSGKILRKLLRNIADGK 601 Query: 602 DWKMPATIDDPAILDEITTALQ 623 ++ +P+TIDDPA L ++ A++ Sbjct: 602 EYGVPSTIDDPASLQDVHEAMK 623 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: 1354 Number of extensions: 60 Number of successful extensions: 4 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