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 BWI76_RS01365 BWI76_RS01365 multifunctional fatty acid oxidation complex subunit alpha
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Koxy:BWI76_RS01365 Length = 729 Score = 183 bits (465), Expect = 2e-50 Identities = 128/367 (34%), Positives = 187/367 (50%), Gaps = 33/367 (8%) Query: 5 VIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ-- 62 V+G+G+MG GIA +A G V M DI+ + L M L+K E G + +G++ Sbjct: 318 VLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERGKI-DGLKMAG 376 Query: 63 VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122 V++ I P D A + D V+EAV E+ ++K+ + E P VLA+NTS++PISE Sbjct: 377 VISTIQPTLDYA-GFERVDVVVEAVVENPKVKKAVLAETEEKVRPDTVLASNTSTIPISE 435 Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182 +ASVL+ P+ GMHFFNP MPLVE++RG TSD+ + A M K IVV D P Sbjct: 436 LASVLQRPENFCGMHFFNPVHRMPLVEVIRGDKTSDKTIAKVVAWASKMGKTPIVVNDCP 495 Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242 GFFVNRVL L+ G A ++VD ++ G+PMG L D G+D + + Sbjct: 496 GFFVNRVLFPYFAGFSQLLRDG-ADFRKVDKVMEKQFGWPMGPAYLLDVVGIDTAHHA-Q 553 Query: 243 AVTARGF-----KAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGK--------------- 282 AV A GF K + + + L + G K+G G+++Y K Sbjct: 554 AVMAAGFPQRMQKEYR-DAIDALFDAKRFGQKNGLGFWRYKEDSKGKPKKEEDTVVDSLL 612 Query: 283 --FVRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---GIL 336 +P + +++ ++ P VNEV L EGI+ +A+ V GLG P G Sbjct: 613 AEVSQPKRDFSDEEIIARMMIPMVNEVVRCLEEGIIASPAEADMALVYGLGFPPFHGGAF 672 Query: 337 SYADEIG 343 + D +G Sbjct: 673 RWLDTLG 679 Score = 114 bits (284), Expect = 2e-29 Identities = 62/180 (34%), Positives = 107/180 (59%), Gaps = 4/180 (2%) Query: 404 EPPLAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEF 463 E +A +V + P N ++ + + +ALD LE+++D++ + + + F GAD+TEF Sbjct: 14 EDGIAELVFDAPGSVNKLDTATVASLGEALDVLEKQKDLKGLLLRSEKAAFIVGADITEF 73 Query: 464 GSLTPVKAMIASRKFH---EVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTA 520 SL V S+ H VF +++ L P I+ +NG ALGGG E L+ D+R+A+ Sbjct: 74 LSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCECVLATDYRLATPDL 133 Query: 521 EMGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL 579 +G PE LG++PG GG+ R+ R+ G LE++ G+ + AE+A ++G+V+ + + E+L Sbjct: 134 RIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDLGAEQALKIGLVDGVVKHEKL 193 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: 1035 Number of extensions: 55 Number of successful extensions: 8 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: 729 Length adjustment: 39 Effective length of query: 612 Effective length of database: 690 Effective search space: 422280 Effective search space used: 422280 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