Align propionate-CoA ligase (EC 6.2.1.17); 3-hydroxypropionyl-CoA synthase (EC 6.2.1.36) (characterized)
to candidate WP_033100144.1 JG50_RS0105805 AMP-binding protein
Query= BRENDA::A4YGR1 (661 letters) >NCBI__GCF_000763315.1:WP_033100144.1 Length = 646 Score = 430 bits (1105), Expect = e-124 Identities = 247/628 (39%), Positives = 373/628 (59%), Gaps = 20/628 (3%) Query: 29 RYYAHLMKLSKEKPAEFWGSLAQDL-LDWYEPWKETMRQEDPM--TRWFIGGKINASYNA 85 R Y + S + A FW + DL L W P+++ + D + TRWF+ GKIN S N Sbjct: 28 RDYDRFYEQSIKNIAWFWDEVVNDLGLRWMMPYRQVLDMSDGIAWTRWFVDGKINISDNC 87 Query: 86 VDRHLNGPR-KFKAAVIWESELGERKIVTYQDMFYEVNRWANALRSLGVGKGDRVTIYMP 144 +DR + P + + A+IWE + G K TY+D++ EVNR A L+ LGV GD V IYMP Sbjct: 88 LDRFVEEPAARHRLALIWEGDDGTTKKYTYRDLWLEVNRLACGLKKLGVAAGDCVAIYMP 147 Query: 145 LTPEGIAAMLASARIGAIHSVIFAGFGSQAIADRVEDAKAKVVITADAYPRRGKVVELKK 204 + E + AMLA ARIGAI + F+G+G++A+A R++ +AK +ITAD Y RRGKVV +K+ Sbjct: 148 MIAENVIAMLAVARIGAIFTPCFSGYGAEAVATRIQGCQAKWLITADGYLRRGKVVAMKE 207 Query: 205 TVDEALNSLGERSP-VQHVLVYRRMKTDVNMKEGRDVFFDEV-GKYRYVEPERMDSNDPL 262 D A + SP V+ V+V R+ D RDV +D++ + + + P D+NDP Sbjct: 208 EADRA----ADLSPSVEKVVVVSRLGRDCPWNPDRDVKWDQLTAEMKTLSPAVTDANDPF 263 Query: 263 FILYTSGTTGKPKGIMHSTGGYLTGTAVMLLWSYGLSQENDVLFNTSDIGWIVGHSYITY 322 I+YTSGTTGKPKG +H G+ A +++ + D+LF +D+GW++G ++ + Sbjct: 264 MIIYTSGTTGKPKGTVHVHSGFPLKAAFDAGYAFDVG-PGDILFWVTDMGWMMG-PWMVF 321 Query: 323 SPLIMGRTVVIYESAPDYPYPDKWAEIIERYRATTFGTSATALRYFMKYGDEYVKNHDLS 382 L++G T++++E PDYP P + E+ E++ T G S T +R MK+G + DLS Sbjct: 322 GTLLLGSTMLVFEGTPDYPIPGRLWELTEKHGVTHLGISPTLIRALMKHGTSWFSQRDLS 381 Query: 383 SIRIIVTNGEVLNYSPWKWGLEVLGGGKVFMSHQWWQTETGAPNLGYLPGIIYMPMKSGP 442 S+R+ + GE N PW W E +GG +V + + TE G L + P+ Sbjct: 382 SLRVFGSTGEPWNPEPWHWLFEQVGGKRVPIFNYSGGTEISG---GILGNHFFKPIVPCG 438 Query: 443 ASGFPLPGNFVEVLDENGNPSAPRVRGYLVMRPPFPPNMMMGMWNDNGERLKKTYFSKFG 502 +G PLPG EV D+ G V G LV+R P+ M G W D R + TY+S++ Sbjct: 439 FAG-PLPGMDAEVFDDQGKTVRGEV-GELVLRQPW-VGMTSGFWQD-ARRYEDTYWSRWP 494 Query: 503 SLYYPGDFAMVDEDGYIWVLGRADETLKIAAHRIGAGEVESAITSHPSVAEAAVIGVPDS 562 + GD+ +VDE G ++ GR+D+TLKIA R+G E+ES + HPSV EAA IGVPD+ Sbjct: 495 KTWLHGDWVIVDEGGQWFITGRSDDTLKIAGKRLGPAEMESVLVDHPSVIEAATIGVPDA 554 Query: 563 VKGEEVHAFVVLKQGYAPSSELAKDIQSHVRKVMGPIVSP-QIHFVDKLPKTRSGKVMRR 621 KGE FVV++ L +++ V + MG + P ++H VD+LPKTR+GK++RR Sbjct: 555 DKGESAVCFVVVRGDGEEVQSLTEELVRFVGERMGKALKPKRVHIVDELPKTRNGKILRR 614 Query: 622 VIKAVMMGSSAGDLTTIEDEASMDEIKK 649 VI+A +G +AGDL+++E+ ++++I++ Sbjct: 615 VIRAAYLGENAGDLSSLENAHAVEKIRR 642 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: 1197 Number of extensions: 72 Number of successful extensions: 7 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: 646 Length adjustment: 38 Effective length of query: 623 Effective length of database: 608 Effective search space: 378784 Effective search space used: 378784 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