Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate HSERO_RS01260 HSERO_RS01260 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q0KEG0 (807 letters) >FitnessBrowser__HerbieS:HSERO_RS01260 Length = 795 Score = 1088 bits (2815), Expect = 0.0 Identities = 549/808 (67%), Positives = 648/808 (80%), Gaps = 14/808 (1%) Query: 1 MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60 +SNFIVKKVAVLGAGVMGAQIAAH INARVPVVLFDLPAKEGPKNGI RAIENLKKLSP Sbjct: 1 VSNFIVKKVAVLGAGVMGAQIAAHCINARVPVVLFDLPAKEGPKNGIVQRAIENLKKLSP 60 Query: 61 APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120 APLG K++A LIQ ANYEDD+A+L+ CDL+IEAIAERMDWKHDLYKKVAPH+ AIFA+ Sbjct: 61 APLGNKDDAALIQVANYEDDLAVLEGCDLIIEAIAERMDWKHDLYKKVAPHIGPKAIFAS 120 Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180 NTSGLSI ALS+GFDA LK+RFCGVHFFNPPRYMHLVELIPT +T+P ILDQLEAFLTTT Sbjct: 121 NTSGLSINALSEGFDAGLKARFCGVHFFNPPRYMHLVELIPTQSTEPHILDQLEAFLTTT 180 Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240 LGKGVVRA DTPNF+ANRVG+F ILA EAEK+G+ DVVDDLTG+KLGRAKS TFRTA Sbjct: 181 LGKGVVRAFDTPNFVANRVGVFGILATIIEAEKYGLSVDVVDDLTGAKLGRAKSGTFRTA 240 Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300 DVVGLDTM HVI+TMQD L DDPF Y TP +L LV+ GALGQK+GAGFYKK GK I Sbjct: 241 DVVGLDTMGHVIRTMQDNLKDDPFFSSYATPPLLAKLVEQGALGQKSGAGFYKKVGKDIL 300 Query: 301 VLDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAV 359 +D G YV G KAD+I+ R+LK KD +R+K L +STNPQ QFLWA+FRD FHYIAV Sbjct: 301 RIDPAKGDYVPGGAKADDIIARILKEKDPVKRMKALHDSTNPQGQFLWAIFRDAFHYIAV 360 Query: 360 YLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAW 419 +LE +A +A D+D A+RWGFGW+ GPFE WQ+AGWKQ+A+WVKED++AGKALS APLP W Sbjct: 361 HLESVADNARDLDFAMRWGFGWSVGPFETWQAAGWKQIAQWVKEDIDAGKALSTAPLPDW 420 Query: 420 VFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVE 479 VF+G GVH+ GS+SP+ ++ VARS+LPVYQRQAFRA + G AAD + AG T Sbjct: 421 VFDG----RDGVHSEKGSYSPSKKADVARSELPVYQRQAFRAPLVGEGAADGKSAGTTFF 476 Query: 480 ENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQL 539 E+++VRIW DDVL++SFK+KM+ IG VIDG+ +A+ AE +KGLV+W P + Sbjct: 477 EDESVRIW--HQNDDVLILSFKTKMHVIGQGVIDGMNKAVSEAEQNFKGLVIWHPDA--- 531 Query: 540 GAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGG 599 A GG FSAGA+L++ +P FM GG K IEP V + Q R+KYASVPV++A +G+ALGG Sbjct: 532 -AEGGAFSAGADLQSMLPLFMSGGVKAIEPVVHQLQQAHQRLKYASVPVIAAVAGLALGG 590 Query: 600 GCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTS 659 GCEL+LH+A RV ++E+YIGLVEVGVGL+PAGGGLKEAA+ AAR A+ +IL FL Sbjct: 591 GCELLLHTAKRVVSIESYIGLVEVGVGLIPAGGGLKEAAVRAAREAK---GNDILPFLKE 647 Query: 660 RFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPTLV 719 +AA A VS SALEAR++GYL+ D IVFN +ELL+VA+ E RAL AGYR LP V Sbjct: 648 YMLAAATANVSKSALEARKLGYLREDDVIVFNPYELLHVAKVEARALFDAGYRPQLPPQV 707 Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779 PV GR+G+ATI A LVNMRDGGFIS HDF + IAE V GG+VE GS+V+E WLL +ER Sbjct: 708 PVIGRNGLATIMAQLVNMRDGGFISAHDFKLGKMIAETVSGGEVEEGSIVNEQWLLDIER 767 Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807 K F++LL KTQERIMGM+QTGKPVRN Sbjct: 768 KFFMELLNHPKTQERIMGMMQTGKPVRN 795 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: 1714 Number of extensions: 71 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: 795 Length adjustment: 41 Effective length of query: 766 Effective length of database: 754 Effective search space: 577564 Effective search space used: 577564 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