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_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_002115805.1:WP_085640004.1 Length = 695 Score = 173 bits (438), Expect = 3e-47 Identities = 132/399 (33%), Positives = 202/399 (50%), Gaps = 29/399 (7%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV-E 61 V VIG G MG GIA +AG V + ++S + A RI +LS + G + + + Sbjct: 291 VAVIGGGTMGAGIATSFLLAGFPVTLLEMSEDAAHAARGRITGNLSGALKRGKIDQKTYD 350 Query: 62 QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121 ++ T L+ +D VIEAV ED+ +KR +F +A P AVLATNTS L I+ Sbjct: 351 RLTGPALALTTSYDDLREADLVIEAVFEDMNVKRDVFSRLDAICKPGAVLATNTSYLDIN 410 Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181 +IA + P+ V+G+HFF+P +M L+E+V T+ + V T +AK + K + Sbjct: 411 KIADATQRPEDVIGLHFFSPAHVMKLLEVVVADRTAPDTVATGFALAKRLKKTAVRAGVC 470 Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241 GF NR+L A ++V G A+ ++D +AI E GF MG F ++D GLDI ++ Sbjct: 471 DGFIGNRILAAYRAAADHMVLDG-ATPYDID-AAIREFGFAMGPFQVSDLAGLDIAWAAR 528 Query: 242 K--AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY----PSPGKFVRPTLPSTSKKL 295 K A T + P + ++L G G K+G GYY Y P P V + S + L Sbjct: 529 KRRAATRDPRERVPLVA-DRLCEAGLFGQKTGQGYYLYNETPPKPNPEVAGIIESARETL 587 Query: 296 G-------------RYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---GILSY 338 G RYL + VNE + ++ +GI + D + ++G G P+ G L + Sbjct: 588 GIKPRAFSRPEIQRRYLCA-MVNEAAKVVGDGIARRPLDVDVVLLMGYGFPRYRGGPLKW 646 Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 AD G+ +++ + Q +SP PLL +V EG+ Sbjct: 647 ADMDGLPKILSDITAYAQDDRY-FWSPAPLLEQLVAEGR 684 Score = 107 bits (267), Expect = 2e-27 Identities = 62/190 (32%), Positives = 115/190 (60%), Gaps = 9/190 (4%) Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466 +A I ++ P NA+ + + + +A++ E + R I G+GR F AGAD+ EFG Sbjct: 13 IAMIAIDNPP-VNALGQAVRQGLVEAVEKAEA-DGARAALIYGEGRSFPAGADIREFGK- 69 Query: 467 TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPE 526 P++ + +V +++ V++ ++G ALGGG+E+AL++D+R+A+ A++G PE Sbjct: 70 PPLEPWLP-----DVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAKVGLPE 124 Query: 527 INLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRK 585 + +G++PG GGTQRL RL G ++++ +GR++ A EA+ LGI++ + + + + Sbjct: 125 VLIGVMPGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRVEDGAPRDIGLSY 184 Query: 586 LANAIAEKSP 595 +AE +P Sbjct: 185 TRALLAENAP 194 Score = 25.8 bits (55), Expect = 0.007 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 3/61 (4%) Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKE-GKLGRKSGQGFHT 388 G G +D G+D+ R+ + D PL+ + E G G+K+GQG++ Sbjct: 507 GFAMGPFQVSDLAGLDIA--WAARKRRAATRDPRERVPLVADRLCEAGLFGQKTGQGYYL 564 Query: 389 Y 389 Y Sbjct: 565 Y 565 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: 942 Number of extensions: 56 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 651 Length of database: 695 Length adjustment: 39 Effective length of query: 612 Effective length of database: 656 Effective search space: 401472 Effective search space used: 401472 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