Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_099019966.1 CCS90_RS12790 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= BRENDA::Q0KEG0 (807 letters) >NCBI__GCF_002591915.1:WP_099019966.1 Length = 788 Score = 760 bits (1963), Expect = 0.0 Identities = 404/805 (50%), Positives = 532/805 (66%), Gaps = 25/805 (3%) Query: 6 VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPAPLGI 65 ++KVA+LGAGVMGAQIAAH NA +P +LFDL AKEGPKNGI +A+ LKKL PAPLG Sbjct: 6 IRKVAILGAGVMGAQIAAHFANAGIPALLFDLAAKEGPKNGIVNKALAGLKKLKPAPLGD 65 Query: 66 KEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATNTSGL 125 LI+ ANY+DD+ LK+ DL+IEA+AERMD K +Y V ++ AIFATNTSGL Sbjct: 66 SAVLSLIEPANYQDDLEKLKQADLIIEAVAERMDIKKSVYDMVEDYINQDAIFATNTSGL 125 Query: 126 SITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTLGKGV 185 SI L+ A L+S+FCGVHFFNPPRYMHLVE+IPT T +++ LE LTT +GKGV Sbjct: 126 SINELATVLPASLQSKFCGVHFFNPPRYMHLVEIIPTNNTDDKVVSDLETVLTTVVGKGV 185 Query: 186 VRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTADVVGL 245 V AKDTPNFIANR+G+FSI++ +FGIPF+ +D LTG+ +GR KSATFRTADVVGL Sbjct: 186 VIAKDTPNFIANRIGVFSIVSTMHHGAEFGIPFETIDALTGTLIGRPKSATFRTADVVGL 245 Query: 246 DTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKVLDAK 305 DT+AH I TM++ L DDP+ ++ P +K L+D GALGQKT AG Y K+G+ I VLD Sbjct: 246 DTLAHTINTMKNGLPDDPWHAHFEQPVWMKALIDKGALGQKTRAGVYMKKGRDILVLDTD 305 Query: 306 TGQYVDAGKKADEIVVRMLKK-DAAERIKLLREST-NPQAQFLWAVFRDVFHYIAVYLEQ 363 G+Y D VV ++KK +R+ L T +PQAQFLW++FRD+FHY A LE Sbjct: 306 KGEYRAQNAALDPRVVEIMKKGKPQDRLTELHALTDSPQAQFLWSIFRDLFHYCATQLEH 365 Query: 364 IAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWVFEG 423 IA +A DID AIRWGFG+ GPFE WQ++GW ++ + +D++AGK ++++P+P+WV Sbjct: 366 IADTARDIDFAIRWGFGYGQGPFETWQASGWNRIVSMIVDDIDAGKTMASSPMPSWVM-- 423 Query: 424 PVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEENDA 483 + G H A GS+S A SF RS VYQRQ F + ++ G T+ E+D Sbjct: 424 ---KVDGAHGAEGSYSAAEDSFKPRSTAAVYQRQLFPDRL----ISEQAHYGETIFEDDD 476 Query: 484 VRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLGAPG 543 +R+W D++ + SFK+K + I V+ GL +A+ +AE YKGL+VWQ Sbjct: 477 IRVW--HQGDEIAIASFKTKKHIIAEGVLKGLRKAVSIAEKDYKGLIVWQTEE------- 527 Query: 544 GPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGGCEL 603 PF+ GANL A A G +E V FQ ++++SVP + A G+ALGGGCE Sbjct: 528 -PFTLGANLAPAAMAISAGQVDAVEQSVDFFQQTSQTLRFSSVPTIMATRGMALGGGCEF 586 Query: 604 MLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSRFQS 663 + + S VAA ETYIGLVE GVGL+PAGGGLKE A R A+ + ++ L F+ Sbjct: 587 SMSATSVVAAFETYIGLVEAGVGLLPAGGGLKE---IARRTAKESFGKDLYPMLEHYFKK 643 Query: 664 AAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPL-PTLVPVA 722 AMA V+ SALEA+Q+G+L+P +IVFN +E+LYVA+ +V+ L GY AP + VA Sbjct: 644 VAMAAVAGSALEAKQIGFLKPCTEIVFNPNEILYVAKAKVKYLHDKGYTAPANEQNIRVA 703 Query: 723 GRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALERKAF 782 G IA ++ L NM +G IS HD+ IA RIA + GG V++ SLV+E +LL LERK F Sbjct: 704 GEPAIANMEMMLANMIEGNMISEHDYEIAKRIAIVMAGGFVDSDSLVTEQYLLDLERKYF 763 Query: 783 VDLLGTGKTQERIMGMLQTGKPVRN 807 ++L+ KT RI L TGKP+RN Sbjct: 764 MELIQMPKTLARIEHTLTTGKPLRN 788 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: 1347 Number of extensions: 56 Number of successful extensions: 8 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: 788 Length adjustment: 41 Effective length of query: 766 Effective length of database: 747 Effective search space: 572202 Effective search space used: 572202 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: 55 (25.8 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