Align propionate-CoA ligase (EC 6.2.1.17); 3-hydroxypropionyl-CoA synthase (EC 6.2.1.36) (characterized)
to candidate CCNA_01017 CCNA_01017 acyl-CoA synthetase
Query= BRENDA::A4YGR1 (661 letters) >FitnessBrowser__Caulo:CCNA_01017 Length = 530 Score = 133 bits (334), Expect = 2e-35 Identities = 156/532 (29%), Positives = 230/532 (43%), Gaps = 59/532 (11%) Query: 108 ERKIVTYQDMFYEVNRWANALRSLGVGKGDRVTIYMPLTPEGIAAMLASARIGAIHSVIF 167 E + T+ + N+ ANAL + G+ GDR+ + +L +A+ G + + I Sbjct: 33 EGRETTFAQLDRHTNQVANALLAAGLSTGDRIAYVGKNSDHYFELLLGAAKAGVVTTPIG 92 Query: 168 AGFGSQAIADRVEDAKAKVVITADAYPRRGKVVELKKTVDEALNSLGERSPVQHVLVYRR 227 + IA V D++AK+V EL VD L R V + + Sbjct: 93 WRLAAPEIAYIVGDSEAKLVFVGR---------ELIGHVDAVAAELTHRPVV--IAMEAE 141 Query: 228 MKTDVNMKEG-RDVFFDEVGKYRYVEPER-MDSNDPLFILYTSGTTGKPKGIM---HSTG 282 D EG RD D V+P + + +D LYTSGTTG+PKG M H+ Sbjct: 142 GAGDYQTFEGWRDAASD-------VDPHKPIQISDIAIQLYTSGTTGRPKGAMLTHHNLL 194 Query: 283 GYLTGTAVMLL-WS-YGLSQENDVLFNTSDIG---W-IVGHSYITYSPLIMGRTVVIYES 336 G A L W+ +G S + V + IG W +VG LI G V+ Sbjct: 195 GMRREAAKNPLEWNQWGPSDVSLVAMPVAHIGGTGWGLVG--------LINGAKGVVARE 246 Query: 337 APDYPYPDKWAEIIERYRATTFGTSATALRYFMKYGDEYVKNHDLSSIRIIVTNGEVLNY 396 P K + IE+ R + AL+ ++ + D S + I+ + Sbjct: 247 FD----PTKVLDFIEKDRISKMFMVPAALQIVVRL--PRAREVDYSRLTHILYGAAPIPL 300 Query: 397 SPWKWGLEVLGGGKVFMSHQWWQTETGAPNLGYLPGIIYMPM--KSGPASGFPLPGNFVE 454 + +EV G G V Q+ TET + YLP + P K A+G P+PG ++ Sbjct: 301 DLLRECMEVFGCGFV---QQYGMTETTG-TVVYLPPEDHDPAGNKRMRAAGLPMPGVELK 356 Query: 455 VLDENGNPSAPRVRGYLVMRPPFPPNMMMGMWNDNGERLKKTYFSKFGSLYYPGDFAMVD 514 ++DE G P G + +R M G W + E KT + GD +D Sbjct: 357 IIDEAGKSLPPNTVGEVAVRSSAN---MAGYWKLD-EATAKTMDAD--GWLRTGDAGYLD 410 Query: 515 EDGYIWVLGRADETLKIAAHRIGAGEVESAITSHPSVAEAAVIGVPDSVKGEEVHAFVVL 574 EDGY+++ R + + I EVESA+ HP VAE AVIGVPD GE V A V Sbjct: 411 EDGYLFIHDRVKDMIISGGENIYPAEVESAVYGHPHVAEVAVIGVPDDKWGEAVKAVVAP 470 Query: 575 KQGYAPSSELAKDIQSHVRKVMGPIVSPQ-IHFVDKLPKTRSGKVMRRVIKA 625 K G P A DI + R + +P+ + F+ LP+ SGK++RR ++A Sbjct: 471 KPGVTPD---ADDIIAFARTRIAHFKAPKSVDFIPALPRNASGKILRRELRA 519 Lambda K H 0.318 0.135 0.408 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: 876 Number of extensions: 48 Number of successful extensions: 5 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: 661 Length of database: 530 Length adjustment: 37 Effective length of query: 624 Effective length of database: 493 Effective search space: 307632 Effective search space used: 307632 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: 53 (25.0 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