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_041096201.1 SUTH_RS00350 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_000828635.1:WP_041096201.1 Length = 653 Score = 184 bits (467), Expect = 1e-50 Identities = 118/333 (35%), Positives = 185/333 (55%), Gaps = 16/333 (4%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERI-KWSLSKLRESGSLKEGVE 61 V V+G+GVMG IA A+ G V + D S E + A+ R K+ KLR+ + ++ Sbjct: 315 VHVVGAGVMGGDIAAWCALRGMTVTLQDQSVERIAPAVGRAAKFFEKKLRDRKLARFALD 374 Query: 62 QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121 +++A + ++ +D +IEA+ E+LE K+ +F + EA A P A+LA+NTSSL ++ Sbjct: 375 RLIA-----DPRGDGVRQADVIIEAIFENLEAKQALFADIEARAKPEALLASNTSSLKLA 429 Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181 +IA+ K P R+VG+HFFNP +MPLVE+V G T+ E + A + ++K + VKD Sbjct: 430 DIAAKFKDPSRLVGIHFFNPVAMMPLVEVVAGAGTAPEAAQKAAAFVRKIDKLPLPVKDA 489 Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241 PGF VN VL M V++GIA E +A+ G PMG LAD GLD+ + Sbjct: 490 PGFLVNAVLAPYMNEAMKCVDEGIA--PETIDAAMLAFGMPMGPIELADTVGLDVAVAAG 547 Query: 242 KAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTL---PSTSKKLGRY 298 + + A P +LV KLG KSG G+Y + GK + + + ++ L + Sbjct: 548 RQLVG---DANPPQKLVELVEGKKLGKKSGQGFYTW-IDGKAQKSKVGAGDTANQALAQR 603 Query: 299 LISPAVNEVSYLLREGIVGKDD-AEKGCVLGLG 330 LI+P ++ L+++G+V + A+ G + G G Sbjct: 604 LITPLLDATQRLVKDGVVADAELADAGVIFGTG 636 Score = 92.4 bits (228), Expect = 6e-23 Identities = 53/185 (28%), Positives = 101/185 (54%), Gaps = 5/185 (2%) Query: 407 LAWIVLNRP-TRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEF-G 464 +AW +L+ + N + D++ E+ LD + +I + + F AGA++ EF Sbjct: 18 VAWAILDTADSSTNTLGADVMAELGLILDECAKHPPKGLIFTSAKEAGFIAGANIEEFVA 77 Query: 465 SLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVA--SKTAEM 522 S TP KA+ ++ +++ ++ ++ P +A++ G +GGG ELAL+ +R+A Sbjct: 78 SDTPEKALALVKRGWDLYNRLAAVSYPTLALVRGHCMGGGTELALACRYRIAVDEPGTRF 137 Query: 523 GQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELES 581 PE+ LG++PG GG RL ++ G +++LTG+ + A+ A ++G+ + P +E+ Sbjct: 138 ALPEVMLGIVPGWGGMLRLPQIVGPAAAFDMMLTGKNIDAKRAKKMGLADECLPPRVMEN 197 Query: 582 EVRKL 586 R L Sbjct: 198 AARML 202 Score = 53.5 bits (127), Expect = 3e-11 Identities = 31/101 (30%), Positives = 55/101 (54%), Gaps = 7/101 (6%) Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTS 358 +++P +NE + EGI + +L G+P G + AD +G+DV V ++ Sbjct: 497 VLAPYMNEAMKCVDEGIA--PETIDAAMLAFGMPMGPIELADTVGLDVAVAAGRQL---- 550 Query: 359 GMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAKYSTI 399 + +P L+ +V+ KLG+KSGQGF+T+ +A+ S + Sbjct: 551 -VGDANPPQKLVELVEGKKLGKKSGQGFYTWIDGKAQKSKV 590 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: 878 Number of extensions: 36 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: 653 Length adjustment: 38 Effective length of query: 613 Effective length of database: 615 Effective search space: 376995 Effective search space used: 376995 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 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