Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase
Query= SwissProt::Q53005 (539 letters) >NCBI__GCF_000423825.1:WP_028989221.1 Length = 652 Score = 148 bits (373), Expect = 7e-40 Identities = 147/562 (26%), Positives = 246/562 (43%), Gaps = 62/562 (11%) Query: 5 DYNAAVDFVDRNVAEGRGGKIAFI-----DPQRSLSYGELRDAVARVGPMLARLGVEQEN 59 + N A + +DR+++ K A I R+ +YG+L V+R +L +LG+ + Sbjct: 81 ELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREVSRFANVLKKLGITTGD 140 Query: 60 RIALVLKDTVDFPILFWGAIRAGIVPVLLNTRLTADQYRYLLEDSRSRVVFASSEFLPVI 119 R+A+ + + + R G + ++ +A+ + +ED++++++ + Sbjct: 141 RVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIEDTQAKLLITADGGF--- 197 Query: 120 EEAAADLPHLR-----TIIAVGDAPAPTLQLANL----------------LATEQEGGAP 158 A + HL+ ++ G + + L L + E P Sbjct: 198 --RAGRVVHLKQHADQALMRDGHSVDKVVVLRRTGQEVDMLDGRDLWWHELMQDAEPQCP 255 Query: 159 AATC-ADDIAYWQYSSGTTGMPKGVMHVHSSPRVMAENAGRRI-GYREDDVVFSAAKLFF 216 A + A+ + Y+SG+TG PKG++H + + R + + +DV + A + + Sbjct: 256 AVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKPEDVYWCTADIGW 315 Query: 217 AYGLGNAMFCPMGIGATSVLY---PERPTADSVFDTLRLHQPTLLFAVPTLYAAMLADPR 273 G A++ P+ +GAT +L+ P P A + + H ++ + PT A++ Sbjct: 316 VTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTAPTAVRALM---- 371 Query: 274 SRTETLPDR-----LRLCVSAGEPLPAQVGLNWRNRFGHD---IVNGVGSTEMGHLFLTN 325 E P + LRL + GEP+ + + + G + +V+ TE G + Sbjct: 372 KLGEEWPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTWWQTETGGHLIAP 431 Query: 326 LPHA--VEYGTSGVPVDGYRLRLVGDRGQDVADDEIGELLVSG----GSSAAGYWNQRDK 379 LP ++ G+ P+ G +V + G V E G LV G + N Sbjct: 432 LPGVTPLKPGSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRPWPGMLRTVWGNDARY 491 Query: 380 TRT---TFVGEWTRTGDKYHRRADGVYTYCGRTDDIFKVSGIWVSPFEIEQALMSHAKVL 436 T F + GD HR ADG Y GR DD+ VSG + EIE AL+SH V Sbjct: 492 LETYWAKFQNRYYVAGDSAHRDADGYYWIMGRIDDVLNVSGHRLGTMEIESALVSHPAVA 551 Query: 437 EAAVI--PAEDTDGLIKPKAFIVL-ASRGDIDPGALFDELKEHVKSAIGPWKYPRWIQIM 493 EAAV+ P E I AF++L S D L + L++HV AIGP P I+ Sbjct: 552 EAAVVGRPHEIKGEAI--TAFVILRQSHVQDDRDRLTEALRQHVSEAIGPIAKPDDIRFT 609 Query: 494 DDLPKTSSGKLQRYLLREMTLG 515 D+LPKT SGK+ R LLR + G Sbjct: 610 DNLPKTRSGKIMRRLLRAIARG 631 Lambda K H 0.320 0.138 0.415 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: 925 Number of extensions: 40 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 539 Length of database: 652 Length adjustment: 37 Effective length of query: 502 Effective length of database: 615 Effective search space: 308730 Effective search space used: 308730 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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