Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate WP_076475473.1 BW971_RS00105 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_900156495.1:WP_076475473.1 Length = 724 Score = 176 bits (445), Expect = 4e-48 Identities = 131/408 (32%), Positives = 203/408 (49%), Gaps = 38/408 (9%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAME-RIKWSLSKLRESGSLKEGV 60 KV VIG+G+MG IA ++A AG +V + D++ E + + + L+ + +E Sbjct: 326 KVGVIGAGMMGAAIAYVSAKAGIDVVLKDVTQEAADKGKQYSVTLEEKALKRGKTTQEKS 385 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 +++LARIHP TD+ + KG DFVIEA E +E+K +F + P AVL +NTS+LPI Sbjct: 386 DELLARIHP-TDKPEDFKGVDFVIEAAFESVEVKNQVFGEIQDIVEPDAVLGSNTSTLPI 444 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 + +A + P+ +G+HFF+P MPLVEI+RG+ TSD V+ + + K IVV D Sbjct: 445 TGLAKGVNRPEDFIGIHFFSPVDKMPLVEIIRGEKTSDAVLAKVIDYTLQIRKTPIVVHD 504 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGI--ASIQEVDSSAIEELGFPMGVFLLADYTGLDIGY 238 GFF +RV+ + V +G+ A I++ S A G+P L+D L + Sbjct: 505 SRGFFTSRVIGTFINEAIAAVGEGVEPARIEQAGSQA----GYPAPPLQLSDELTLTLMQ 560 Query: 239 SVWKAVTARGFKA----FPCSST----EKLVSQGKLGVKSGSGYYQYPSPGK------FV 284 + KA T G+KA FP + ++LV G+ K G G+Y Y GK + Sbjct: 561 KIRKA-TEEGYKAEGKDFPDHGSYEVIDRLVEAGRTSKKDGKGFYDYDDAGKRTGLWPGL 619 Query: 285 RPTLPSTSKKL------GRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GI 335 R S S + R L + A+ V + +DA G + G+G P G+ Sbjct: 620 RDEFKSGSGDVPFIDLQERMLFAEALETVRCFDEGVLTSVEDANIGSIFGIGFPPWTGGV 679 Query: 336 LSYADEI--GIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGKLGRK 381 + Y ++ G+ V+ E+ G P S+V++ K G K Sbjct: 680 IQYINQYSGGLQGFVDRANELAARYGQQFVPP----TSLVEKAKAGEK 723 Score = 90.9 bits (224), Expect = 2e-22 Identities = 59/175 (33%), Positives = 94/175 (53%), Gaps = 14/175 (8%) Query: 419 NAINGDMIREINQALDSLE-EREDVRVIAITGQGRVFSAGADVTEFGSLT--------PV 469 N +N + I +D LE E++ + + IT + F AG D+ E + + Sbjct: 28 NTMNALFLESIGPIVDRLEAEKDSITGVVITSAKKTFFAGGDLKEMTADQGDRPKEDIAL 87 Query: 470 KAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVAS--KTAEMGQPEI 527 + ++ + +++ L KPV+A +NG ALGGG+ELAL R+A+ K ++G PE+ Sbjct: 88 EITNSTNAMKKSLRRLETLGKPVVAAVNGAALGGGLELALHTHHRIAADVKGNQLGLPEV 147 Query: 528 NLGLIPGGGGTQRLSRLSGRKG--LELVLTGRRVKAEEAYRLGIV-EFLAEPEEL 579 LGL+PGGGG R RL G + + ++L G R K +A +G+V E + EEL Sbjct: 148 QLGLLPGGGGVTRTVRLLGVQTALMSVLLQGNRFKPAKAKEIGLVDEVVGSVEEL 202 Score = 27.3 bits (59), Expect = 0.002 Identities = 26/106 (24%), Positives = 47/106 (44%), Gaps = 16/106 (15%) Query: 291 TSKKLGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDV---V 347 TS+ +G + +NE + EG+ + G G P L +DE+ + + + Sbjct: 510 TSRVIGTF-----INEAIAAVGEGVEPARIEQAGSQAGYPAPP--LQLSDELTLTLMQKI 562 Query: 348 VNTLEEMRQTSGMDHYSPD----PLLLSMVKEGKLGRKSGQGFHTY 389 EE + G D PD ++ +V+ G+ +K G+GF+ Y Sbjct: 563 RKATEEGYKAEGKDF--PDHGSYEVIDRLVEAGRTSKKDGKGFYDY 606 Lambda K H 0.316 0.134 0.377 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: 1050 Number of extensions: 50 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 651 Length of database: 724 Length adjustment: 39 Effective length of query: 612 Effective length of database: 685 Effective search space: 419220 Effective search space used: 419220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 54 (25.4 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