Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_092482981.1 BM299_RS08140 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= BRENDA::Q0KEG0 (807 letters) >NCBI__GCF_900115975.1:WP_092482981.1 Length = 807 Score = 488 bits (1255), Expect = e-142 Identities = 313/828 (37%), Positives = 443/828 (53%), Gaps = 51/828 (6%) Query: 6 VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAK-------------EGP--KNGIALR 50 + K AVLGAGVMGA IAAHL N +P L D+ E P +N +A Sbjct: 5 INKAAVLGAGVMGATIAAHLANVGIPTYLLDIVPNQLTPEEEKKGLTLESPQVRNRLATG 64 Query: 51 AIENLKKLSPAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAP 110 AI + K PAP + E A L+ N+ED++ +L ECD +IE + ER+D K L+KKV Sbjct: 65 AIGAMLKAKPAPFYVPENAALLTPGNFEDNMDVLAECDWIIEVVVERLDIKQSLFKKVEA 124 Query: 111 HLASHAIFATNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQIL 170 +I A+NTSG+SI + +G + K F G HFFNPPRYM L+ELIP + T P++L Sbjct: 125 VRRPGSIVASNTSGISINKMCEGLSQEFKQHFLGAHFFNPPRYMKLLELIPCSETLPEVL 184 Query: 171 DQLEAFLTTTLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLG 230 + + F LGKGVV KDTPNFIANR+G++ + A FG+ + VD LTG L Sbjct: 185 EFMRDFGERILGKGVVICKDTPNFIANRIGVYGMCATIKAMLDFGLTVEEVDALTGRALC 244 Query: 231 RAKSATFRTADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAG 290 R KSA+FRT D+VGLD M HV K + D + V++TP L+ +++ LG KT G Sbjct: 245 RPKSASFRTLDMVGLDVMVHVAKNVYDVATEPAEKAVFETPEFLQKMLENKWLGDKTKQG 304 Query: 291 FYKK----EGKAIKVLDAKTGQYVDAGK-KADEIVVRMLKKDAAERIKLLRESTNPQAQF 345 FYKK +G+ I VLD +Y K K + A+++K L + A+F Sbjct: 305 FYKKVKTDKGREILVLDYNAMEYRPKEKPKFASLEAAKQAGKPAKQMKTLVFGKDKGAEF 364 Query: 346 LWAVFRDVFHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDV 405 W V ++ Y A L +IA ID A++WGF W+ GPFE W G ++VA+ +K + Sbjct: 365 AWRVQKETIVYAANLLGEIADDIQSIDDAMKWGFNWDFGPFEVWDILGVQEVADRIKAE- 423 Query: 406 EAGKALSAAPLPAWVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKG 465 +P V E A G + + F SK V +R +G Sbjct: 424 -------GGTVPKVVEELLAAGRTGFYEKKDGY---RYYFEQNSKESVRER-----IPEG 468 Query: 466 TAAADPRKAGRTVEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAG 525 P K V ++++ + G D V + F SK N IG D+++ + ++ E Sbjct: 469 IIFLAPLKEQNKVIKSNSGASLIDIG-DGVACLEFHSKANAIGDDIVNMINYSVKEVEQN 527 Query: 526 YKGLVVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYAS 585 Y+GLV+ G G FS GANL + ++ V FQ MR+KY Sbjct: 528 YEGLVI--------GNFGQHFSVGANLFLILMEAEDDEFDELDIMVDEFQKANMRLKYCK 579 Query: 586 VPVVSAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAA--- 642 PVV+A G+ +GGGCE+ LH+ AA ETY+GLVEVGVGLVP GGG KE A AA Sbjct: 580 KPVVAAPHGMTVGGGCEVCLHAHRVNAAGETYMGLVEVGVGLVPGGGGCKELAFRAAELM 639 Query: 643 --RAAQAAGSTNILQFLTSR-FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVA 699 ++ G TN +Q + +R F++ AMAKV+ S EA + GY++P+D++ N ++ A Sbjct: 640 PPKSQVTTGGTNTVQPMINRAFENIAMAKVATSGYEAIKFGYMRPTDRVSPNRDRIIGDA 699 Query: 700 QNEVRALASAGYRAPLPTLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVC 759 + V +A+ G++ P + G +G A I+ + + G IS HD IA ++A + Sbjct: 700 KRMVLQMAANGFKPLQPKKMQAVGNAGYAAIELGIQTLLWGKQISEHDAKIAKKVAYILT 759 Query: 760 GGDVEAGSLVSEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807 GG V G+ V+E LL LER+AF+ LLG KT +R+ ML+ KP+RN Sbjct: 760 GGGVTPGTEVTEQDLLDLEREAFLSLLGEPKTLDRMRYMLKYNKPLRN 807 Lambda K H 0.319 0.134 0.391 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: 1332 Number of extensions: 55 Number of successful extensions: 6 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: 807 Length of database: 807 Length adjustment: 41 Effective length of query: 766 Effective length of database: 766 Effective search space: 586756 Effective search space used: 586756 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: 56 (26.2 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