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_036259721.1 DL86_RS06940 fatty acid oxidation complex subunit alpha FadB
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_000746085.1:WP_036259721.1 Length = 720 Score = 190 bits (483), Expect = 2e-52 Identities = 130/374 (34%), Positives = 196/374 (52%), Gaps = 31/374 (8%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60 K V+G+GVMG GIA +A G + M DI+ + L M + L++ E G L + Sbjct: 319 KAAVVGAGVMGGGIAYQSAARGVPIIMKDIAEQALDLGMSEARKLLARQVEQGRLDQAKA 378 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 + +L I P + G D VIEAV E++ +K+ + E +A+LA+NTSSL I Sbjct: 379 DAILGAIAPGLTY-EGFDGVDVVIEAVVENIAVKKAVLSELERVTGEAAILASNTSSLRI 437 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 ++ L+ P + +GMHFFNP M LVE+VRG TS+E + T A +M K IV++D Sbjct: 438 GDLTEGLRRPDKFIGMHFFNPVPRMALVEVVRGPKTSEETIATIVGYADAMGKTPIVMQD 497 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 PGF VNR L + A LV G A VD +E G+PMG L D G+DI + V Sbjct: 498 CPGFVVNRALTPYLIAFLRLVHDG-ADFAHVD-KVMETFGWPMGPAYLIDVIGMDISHHV 555 Query: 241 WKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQY-------------PSPGKF 283 + V+A GF + S+ + L+ + +LG K+G G+Y+Y P + Sbjct: 556 VEIVSA-GFPERMQTSFASAIDILLREKRLGQKNGHGFYKYAKDAKGRPRKELDPETDRL 614 Query: 284 VRPTLPSTSKKLG-----RYLISPAVNEVSYLLREGIVG-KDDAEKGCVLGLGLPK---G 334 + P+ +G ++ P + E + + +G+VG + +A+ +LGLGLP+ G Sbjct: 615 LAEARPNGKIAIGEDEIVERMMLPLIFEAARCVEDGVVGSRGEADMSLILGLGLPRYLGG 674 Query: 335 ILSYADEIGIDVVV 348 L YAD +G+ VV Sbjct: 675 ALKYADHLGVANVV 688 Score = 103 bits (258), Expect = 2e-26 Identities = 63/169 (37%), Positives = 92/169 (54%), Gaps = 8/169 (4%) Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL-----TPVKAMI 473 N ++ E+ +AL+ + ++ + I F GAD+ EF ++ + A + Sbjct: 34 NKLDALTFSELRRALEIIAATPAIKGVLIASAKDAFIVGADIFEFTAIFKRPPEDIVAFV 93 Query: 474 ASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEINLGLIP 533 A E+ + L P +A INGLALGGG+ELAL+ADFRV S A +G PE++LGL P Sbjct: 94 AQNS--EIITALADLPVPTVAAINGLALGGGLELALAADFRVMSSAARIGFPEVHLGLFP 151 Query: 534 GGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELES 581 G GGT RL RL G E + +G + K E A G V+ + PE+L + Sbjct: 152 GYGGTVRLPRLIGLVASAEWIASGAQQKPEAALEEGAVDAVVAPEDLRA 200 Score = 30.0 bits (66), Expect = 4e-04 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 13/70 (18%) Query: 330 GLPKGILSYADEIGIDVVVNTLE-------EMRQTSGMDHYSPDPLLLSMVKEGKLGRKS 382 G P G D IG+D+ + +E E QTS S +LL +E +LG+K+ Sbjct: 535 GWPMGPAYLIDVIGMDISHHVVEIVSAGFPERMQTS---FASAIDILL---REKRLGQKN 588 Query: 383 GQGFHTYAHE 392 G GF+ YA + Sbjct: 589 GHGFYKYAKD 598 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: 977 Number of extensions: 51 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: 720 Length adjustment: 39 Effective length of query: 612 Effective length of database: 681 Effective search space: 416772 Effective search space used: 416772 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