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 16447 b2341 fused enoyl-CoA hydratase and epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase (NCBI)
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Keio:16447 Length = 714 Score = 164 bits (416), Expect = 1e-44 Identities = 126/398 (31%), Positives = 199/398 (50%), Gaps = 28/398 (7%) Query: 3 VTVIGSGVMGHGIAELAAI-AGNEVWMNDISTEILQQAMERIKWSL--SKLRESGSLKEG 59 V ++G G+MG GIA + A AG V + DI+ + + A+ + W K+R Sbjct: 311 VGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHAL-KYSWDQLEGKVRRRHLKASE 369 Query: 60 VEQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLP 119 ++ LA I TD + D +IEAV E+LELK+ + E + + + A+NTSSLP Sbjct: 370 RDKQLALISGTTDY-RGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSLP 428 Query: 120 ISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVK 179 I +IA+ P++V+G+HFF+P MPLVEI+ TS + + TT ++AK K IVV+ Sbjct: 429 IGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVVR 488 Query: 180 DVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYS 239 D GF+VNR+L + ++ +G ++ +D +A+ + GFP+G L D G+D G Sbjct: 489 DKAGFYVNRILAPYINEAIRMLTQG-ERVEHID-AALVKFGFPVGPIQLLDEVGIDTGTK 546 Query: 240 VWKAVTARGFKAF--PCSSTEKLVSQGKLGVKSGSGYYQYPSPG----KFVRPTLPSTSK 293 + + A + F P + +++ + G K+G G+Y Y G K V P + Sbjct: 547 IIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPLIG 606 Query: 294 KLGRYLIS-PAVNE--VSYLLREGIVGKD--------DAEKGCVLGLGLPK---GILSYA 339 G+ IS P V E V +L E + D D + G V G+G P G Y Sbjct: 607 TQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYI 666 Query: 340 DEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 D +G VV ++ + G ++P L+ M G+ Sbjct: 667 DSLGAGEVVAIMQRLATQYG-SRFTPCERLVEMGARGE 703 Score = 105 bits (261), Expect = 9e-27 Identities = 75/218 (34%), Positives = 123/218 (56%), Gaps = 8/218 (3%) Query: 398 TIVVRVEPPLAWIVLNRP-TRYNAINGDMIREINQALDSLEEREDVR-VIAITGQGRVFS 455 T+ VR++ +A I ++ P + N + + ++ + L E +++R V+ ++ + F Sbjct: 8 TLNVRLDN-IAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 Query: 456 AGADVTEFGSL-TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFR 514 AGAD+ G+ T +A +R+ ++ +I L VIA I+G LGGG+ELAL+ R Sbjct: 67 AGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGR 126 Query: 515 VASKTAE--MGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVE 571 V + + +G PE+ LGL+PG GGTQRL RL G LE++LTG++++A++A +LG+V+ Sbjct: 127 VCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVD 186 Query: 572 FLAEPEELESEVRKLANAIAEKS-PLAVASAKLAYKLG 608 + L +LA S PL V LA LG Sbjct: 187 DVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLG 224 Score = 46.2 bits (108), Expect = 5e-09 Identities = 24/97 (24%), Positives = 49/97 (50%), Gaps = 2/97 (2%) Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTS 358 +++P +NE +L +G + + ++ G P G + DE+GID + + Sbjct: 498 ILAPYINEAIRMLTQG--ERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAY 555 Query: 359 GMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAK 395 G +P ++ S++ + + GRK+G+GF+ Y + K Sbjct: 556 GERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRK 592 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: 922 Number of extensions: 38 Number of successful extensions: 7 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: 714 Length adjustment: 39 Effective length of query: 612 Effective length of database: 675 Effective search space: 413100 Effective search space used: 413100 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 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