Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 3610445 Dshi_3826 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::P07896 (722 letters) >FitnessBrowser__Dino:3610445 Length = 673 Score = 381 bits (978), Expect = e-110 Identities = 244/681 (35%), Positives = 363/681 (53%), Gaps = 37/681 (5%) Query: 11 LAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFT 70 LA + + NPPVNA S V + + + + + AI+ C A F AG D+ F A Sbjct: 15 LAWVTVDNPPVNATSTAVRQGLLDAVTRVQGARL--AILRC-AGRTFIAGGDMREFDAPP 71 Query: 71 PGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILP 130 L +VD I+ P +A +QG LGGGLE+A+GC YRIA R GLPEVT+G++P Sbjct: 72 QPPDLPDVVDAIEASATPFVAVMQGTVLGGGLEIAMGCAYRIAAPGTRFGLPEVTVGLIP 131 Query: 131 GARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDK 190 GA GTQ PR+ G A+D+ +GK LSA EA G LDA+ +D E A A+ ++ + Sbjct: 132 GAGGTQRAPRLFGWDAAIDMACAGKLLSAQEAHARGALDAI--ADDPEAA---ARALVPE 186 Query: 191 PIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGIKE 250 P P + +P P P+ + A + + G AP + ++ + P+ G ++ Sbjct: 187 PRIP--VSERPAPPPPDSARIAAHR-RTLAARARGQTAPLQALDALLWATG-PFREGQRK 242 Query: 251 EEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGTMGRG 310 E L + LRAS Q++AL++AFFAE++ + A + + + ++ + V+G G MG G Sbjct: 243 ERALHLSLRASDQSRALRHAFFAERTVAR-----PAVIRDRTPREIARIAVMGGGLMGAG 297 Query: 311 IAISFARVGISVVAVESDPKQLDAAKK----IITFTLEK-EASRAHQNGQASAKPKLRFS 365 IA + G V +E D +AA+ +I L + + +A + +A LR Sbjct: 298 IAAACLGAGYRVDLLERDAATAEAARDRVRGLIAGALRRGKIDQARHDAHCAA---LRTG 354 Query: 366 SSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQ 425 + DL +EAVFE+ K+ FA L+ + P A L TNTS L+ +I + P Sbjct: 355 VGIGHAAEADLAIEAVFEETATKRAAFAALAQVMAPDAILATNTSYLDPREIFAGIPAPD 414 Query: 426 LVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLA 485 +G HFF+PAHVM+LLEV+ +S T+AT +L+ ++ K+ V+ G C GF+GNRMLA Sbjct: 415 RCLGLHFFAPAHVMKLLEVVRLPETSAETLATAFALAGRLRKVAVLSGICDGFIGNRMLA 474 Query: 486 PYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPP 545 Y ++L +G+ PE +DG + +G MGPF DL+GL + R+ Q T P+ Sbjct: 475 AYRRAAEYMLADGALPEQIDGAMRAYGMAMGPFEAQDLSGLHIAEANRRRQDATRPA--- 531 Query: 546 GTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREV 605 RY L D LC GR GQ+ GKGWY Y + R + DP ++ ++ Y Sbjct: 532 --------RERYVTLSDQLCALGRTGQRAGKGWYAYAEG-DRRPRVDPAVTALITDYSAA 582 Query: 606 HHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFY 665 H + +RT EI R L L NE R++EEG+A +D++ LHGYG+PR +GGP+F Sbjct: 583 HGLPRRTHDAGEIQARLLAVLANEGARLVEEGIADSDAAVDMVKLHGYGFPRWRGGPLFA 642 Query: 666 AASVGLPTVLEKLQKYYRQNP 686 A G T+ L +P Sbjct: 643 ARQAGDATIRAALDALDAASP 663 Lambda K H 0.319 0.136 0.405 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: 1023 Number of extensions: 54 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 722 Length of database: 673 Length adjustment: 39 Effective length of query: 683 Effective length of database: 634 Effective search space: 433022 Effective search space used: 433022 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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