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 PP_2047 PP_2047 3-hydroxyacyl-CoA dehydrogenase family protein
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Putida:PP_2047 Length = 412 Score = 169 bits (429), Expect = 2e-46 Identities = 133/408 (32%), Positives = 207/408 (50%), Gaps = 32/408 (7%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60 +V VIG+G MG GI A AG V D + L+ + + + ++ + + + Sbjct: 9 QVAVIGAGTMGRGIVISLANAGLSVLWLDCNAAALEAGLGMVSQAWAQQVDKQRITQAQA 68 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 + LAR+ D AL +D VIEAV E+L LK+ IF +AH P A+LA+NTS+L I Sbjct: 69 DACLARVQA-VDGYPALAEADLVIEAVYENLALKQEIFCALDAHLKPRAILASNTSALDI 127 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 IA+V + P +V+G+HFF+P +M L+EIVRG T +V+ + + M K IV + Sbjct: 128 DAIAAVTQRPSQVLGLHFFSPAHVMKLLEIVRGTHTDQKVLDAAKALGERMGKVAIVAGN 187 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 PGF NR+L + L+ +G A +VD + +++ GF MG F + D G+D+ + Sbjct: 188 CPGFIGNRMLRSYVGEARKLLLEG-ALPHQVD-AVLQQFGFAMGPFRMYDVVGIDLEWRA 245 Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGK-------FVRPTLPSTSK 293 + + +G L G+LG K+G GYY+Y +PG V + S+ Sbjct: 246 -RQLAGQGMHDPLVQVDNALCELGRLGQKTGQGYYRY-APGSRQAEHDPQVDALVLQVSQ 303 Query: 294 KLG-------------RYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---GIL 336 LG R L++ VNE + +L+EGI D ++ + G G P G + Sbjct: 304 NLGYRRRGISAEEILERCLLA-LVNEGAKVLQEGIAASSGDIDQVWLHGYGFPAATGGPM 362 Query: 337 SYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGKLGRKSGQ 384 +ADE G ++ LE ++ G +H+ P LL S+V GK G+ Sbjct: 363 RWADEQGAPFILARLEYLQGVLG-EHWRPAGLLYSLVAGGKRFEPRGE 409 Score = 33.1 bits (74), Expect = 2e-05 Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 11/99 (11%) Query: 295 LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEM 354 +G ++ V E LL EG + + G G D +GID+ Sbjct: 192 IGNRMLRSYVGEARKLLLEGALPHQ--VDAVLQQFGFAMGPFRMYDVVGIDLEWRA---- 245 Query: 355 RQTSGMDHYSPDPLLL---SMVKEGKLGRKSGQGFHTYA 390 RQ +G + DPL+ ++ + G+LG+K+GQG++ YA Sbjct: 246 RQLAGQGMH--DPLVQVDNALCELGRLGQKTGQGYYRYA 282 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: 559 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 651 Length of database: 412 Length adjustment: 35 Effective length of query: 616 Effective length of database: 377 Effective search space: 232232 Effective search space used: 232232 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: 52 (24.6 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