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_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_002117405.1:WP_085772004.1 Length = 728 Score = 176 bits (446), Expect = 3e-48 Identities = 125/404 (30%), Positives = 201/404 (49%), Gaps = 38/404 (9%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV- 60 K+ V+G+G MG G+ ++A+ G EV + D Q++ ++ K ++ KL SG + G Sbjct: 329 KIGVLGAGFMGAGVGYVSALNGLEVVLIDRD----QESADKGKATIDKLI-SGQVSRGKA 383 Query: 61 -----EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNT 115 E +LAR+ D + LKG D ++EAV ED +K + A+A P V A+NT Sbjct: 384 TASAKEALLARVEATPDY-ERLKGCDLILEAVFEDRAVKAEATKRAQAAVGPDVVFASNT 442 Query: 116 SSLPISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKET 175 S+LPI+ +A P+ +G+HFF+P M LVEI+ G+ TSD+ + T + + + K Sbjct: 443 STLPITSLAETSLKPENFIGVHFFSPVEKMLLVEIILGEKTSDKALATALDFVRMIKKTP 502 Query: 176 IVVKDVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLD 235 IVV D GFF NR +L + G ++ +G+ + +A G P+G L D GLD Sbjct: 503 IVVNDSRGFFANRCVLAYVREGQTMLVEGVP--PAMIENAARMAGMPVGPLSLNDEVGLD 560 Query: 236 IGYSVWKAVTARGFKAFPCSSTEKLV------SQGKLGVKSGSGYYQYPSPG-KFVRPTL 288 +G+ + +A T + A ++ V G+ G K+G G+Y YP+ G K + P L Sbjct: 561 LGWKILQA-TKKDLGAAAVDPAQERVLGFLVEKNGRFGRKNGKGFYDYPASGKKTLWPGL 619 Query: 289 PSTSKKL------------GRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK--- 333 ++K R+L++ AV + +A+ G +LG G Sbjct: 620 AGLAEKTLDPDAIDVKELERRFLVAQAVEAARTFAEHVVTDPREADVGSILGFGFAPFTG 679 Query: 334 GILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 G LSY D +G+ V + + G ++P LL M +EG+ Sbjct: 680 GALSYIDGMGLKAFVALCDTLAAKYG-PRFAPPQLLRDMAREGE 722 Score = 73.6 bits (179), Expect = 3e-17 Identities = 49/184 (26%), Positives = 88/184 (47%), Gaps = 18/184 (9%) Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVT--------------EFG 464 N I +++ E+ Q ++ + ++ I FS GAD++ E G Sbjct: 28 NVITEEVMSELAQVVEKVAADAAIKGCVIASGKNAFSGGADLSMLQKSRAAHGKALGEKG 87 Query: 465 SLTPVKAMIAS-RKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKT--AE 521 + + S RK +++ +++ KP I+G+ LGG ELAL+ RV + + Sbjct: 88 AEEANRLFFESARKLSQLYRRLETCGKPFAIAIHGVCLGGAFELALACHHRVLADDDKTK 147 Query: 522 MGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELE 580 +G PE+ +GL PG GGTQR++R+ L+ + G ++ + A G+ + LA E+ Sbjct: 148 VGLPEVKVGLFPGAGGTQRVARIMPTGDALQFLFKGEQLSGKAAKAAGLAQELAPQSEIV 207 Query: 581 SEVR 584 S + Sbjct: 208 SRAK 211 Score = 39.7 bits (91), Expect = 5e-07 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%) Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDP---LLLSMVKEGKLGRKSGQGF 386 G+P G LS DE+G+D+ L+ ++ G P L + K G+ GRK+G+GF Sbjct: 545 GMPVGPLSLNDEVGLDLGWKILQATKKDLGAAAVDPAQERVLGFLVEKNGRFGRKNGKGF 604 Query: 387 HTY 389 + Y Sbjct: 605 YDY 607 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: 975 Number of extensions: 48 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: 728 Length adjustment: 39 Effective length of query: 612 Effective length of database: 689 Effective search space: 421668 Effective search space used: 421668 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