Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Ac3H11_1914 Enoyl-CoA hydratase (EC 4.2.1.17) / 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
Query= BRENDA::Q0KEG0 (807 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1914 Length = 800 Score = 974 bits (2519), Expect = 0.0 Identities = 500/810 (61%), Positives = 611/810 (75%), Gaps = 13/810 (1%) Query: 1 MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60 MS F VKKVAVLGAGVMGAQIAAHL+N +VPVVLFDLPAKEGPKNGI +A+E LKKL P Sbjct: 1 MSRFQVKKVAVLGAGVMGAQIAAHLVNVKVPVVLFDLPAKEGPKNGIVTKAVEGLKKLKP 60 Query: 61 APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120 +PLG+ ++A LIQ ANYE+ + LLKECDLVIEAIAERMDWK DLY K+APH+A HAI A+ Sbjct: 61 SPLGLADDAALIQQANYEEHMHLLKECDLVIEAIAERMDWKLDLYTKIAPHVAKHAILAS 120 Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180 NTSGLSIT LS+ +K RFCG+HFFNPPRYM LVELI T TTQP++LDQLEAF+T+ Sbjct: 121 NTSGLSITKLSEVLPESIKPRFCGIHFFNPPRYMTLVELINTPTTQPEVLDQLEAFVTSG 180 Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240 LGKGVVRA DTPNF+ANRVGI +LA E E FG+ +DVVDDLTG KLGRA S TFRTA Sbjct: 181 LGKGVVRAHDTPNFVANRVGIAGMLATMKEVENFGLTYDVVDDLTGKKLGRASSGTFRTA 240 Query: 241 DVVGLDTMAHVIKTMQDTL--HDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKA 298 DVVGLDTMAHVIKT+QD L DPF + TPAVLK L++ G LGQK AGF+KK G+ Sbjct: 241 DVVGLDTMAHVIKTLQDNLSIETDPFYESFGTPAVLKKLLELGNLGQKAKAGFFKKVGRD 300 Query: 299 IKVLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358 + + + +YV AG+KADE+ RMLKK AAER++LLR + QFLWA+ R+ FHY A Sbjct: 301 VMRFELDSEEYVPAGQKADEVYSRMLKKPAAERLRLLRNAEGAPGQFLWAILRNSFHYAA 360 Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418 V+L IA +A D+D A+RWGFG GPFE WQ AGW +VA+ ++ED++AGKAL APLP Sbjct: 361 VHLGTIADNARDVDQAMRWGFGMKQGPFELWQEAGWLEVAKMIQEDIDAGKALCKAPLPE 420 Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKG-TAAADPRKAGRT 477 WVF+GPVAE GVH A GSWS + FV R +LPVY+RQ F A+ G T+ D R AG T Sbjct: 421 WVFKGPVAEAAGVHTAQGSWSASQNKFVPRRQLPVYERQIFPEALLGETSLPDWRTAGTT 480 Query: 478 VEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSL 537 + E+ A+R W +GQ VL+ S K+KM+ I P+V++ L A++LAE+ Y+G+V+W Sbjct: 481 IAESKALRTWTLDGQ--VLIASIKNKMHAISPEVMEALMEALELAESEYQGMVIW----- 533 Query: 538 QLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIAL 597 + PFS GA+LEA MPAFM+GGA +E + Q+ MMR++YA VPVV+A G+AL Sbjct: 534 ---SGDAPFSVGADLEATMPAFMVGGADAVESIEQELQNLMMRIRYAQVPVVAAIHGMAL 590 Query: 598 GGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFL 657 GGGCEL ++SA RVA +E+YIGLVEVGVGLVP GGL A AA A+ S +IL FL Sbjct: 591 GGGCELAVYSAKRVAHMESYIGLVEVGVGLVPGAGGLTYIARRAAENMAASTSKDILPFL 650 Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT 717 T F +AAMAKV SALE+R++G+L D IV + ELL+VA NE +++A++G+ AP Sbjct: 651 TEGFTAAAMAKVGTSALESRKLGFLLDGDVIVPHKDELLFVAINEAKSMAASGWCAPHKR 710 Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777 L PVAGRSG+ATIKA LVNMRDGGFIS +DF I + IAE VCGGDV+AGS+VSE++LL L Sbjct: 711 LFPVAGRSGLATIKAQLVNMRDGGFISAYDFKIGAMIAEVVCGGDVDAGSMVSEEYLLTL 770 Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807 ERK F L+ KT ERI+GML TGKPVRN Sbjct: 771 ERKVFCHLIAQPKTHERILGMLSTGKPVRN 800 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: 1599 Number of extensions: 62 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: 807 Length of database: 800 Length adjustment: 41 Effective length of query: 766 Effective length of database: 759 Effective search space: 581394 Effective search space used: 581394 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 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