Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 3610445 Dshi_3826 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Dino:3610445 Length = 673 Score = 469 bits (1208), Expect = e-136 Identities = 288/674 (42%), Positives = 391/674 (58%), Gaps = 37/674 (5%) Query: 9 TQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68 T +A VTVD+PPVNA S AVR+G+L+ V + +L CAGRTFIAG D+ EF Sbjct: 11 TDTGLAWVTVDNPPVNATSTAVRQGLLDAVTRV---QGARLAILRCAGRTFIAGGDMREF 67 Query: 69 GKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKL 128 PPQPP L DV+ A+E S P +A + GT LGGGLE+A+GC +R+A + GLPEV + Sbjct: 68 DAPPQPPDLPDVVDAIEASATPFVAVMQGTVLGGGLEIAMGCAYRIAAPGTRFGLPEVTV 127 Query: 129 GLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVAGAVAFAK-- 186 GL+PGAGGTQR PR G + A+ M G + A EA G ++ + ++ A A A Sbjct: 128 GLIPGAGGTQRAPRLFGWDAAIDMACAGKLLSAQEAHARGALDAIADDPEAAARALVPEP 187 Query: 187 KVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLP 246 ++ +RP D +++AA + + +ARG AP DA+ A P Sbjct: 188 RIPVSERPAPP-PPDSARIAAHRR----------TLAARARGQTAPLQALDALLWATG-P 235 Query: 247 FEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTM 306 F EG +KER + L SDQS+A R+AFFAER A+ + D T PR ++R+A++G G M Sbjct: 236 FREGQRKERALHLSLRASDQSRALRHAFFAERTVARPAVIRDRT-PREIARIAVMGGGLM 294 Query: 307 GGGIAMSFANAGIPVTLIE----TGEEQLKRGLGIMQKNWEATAARGGLPPDA--PAKRM 360 G GIA + AG V L+E T E R G++ A A R G A A Sbjct: 295 GAGIAAACLGAGYRVDLLERDAATAEAARDRVRGLI-----AGALRRGKIDQARHDAHCA 349 Query: 361 ALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAA 420 AL TG VG+ + +ADL IEAVFE A K+ F A+ P A+LA+NTSYL EI A Sbjct: 350 ALRTG-VGIGHAAEADLAIEAVFEETATKRAAFAALAQVMAPDAILATNTSYLDPREIFA 408 Query: 421 TTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFV 480 P LG+HFF+PA+VMKL E+VR +T+ + L TA ++A ++ KV V+ G+CDGF+ Sbjct: 409 GIPAPDRCLGLHFFAPAHVMKLLEVVRLPETSAETLATAFALAGRLRKVAVLSGICDGFI 468 Query: 481 GNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK 540 GNRMLAA + +E +L +GALP+Q+D + +GM MGPF DL+GL I +R+ + Sbjct: 469 GNRMLAAYRRAAEYMLADGALPEQIDGAMRAYGMAMGPFEAQDLSGLHIAEANRRRQDAT 528 Query: 541 S-------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRR 593 ++D LC GR GQ+ GKG+Y Y +G R P DP V LI D A GL RR Sbjct: 529 RPARERYVTLSDQLCALGRTGQRAGKGWYAYAEGDRRPRVDPAVTALITDYSAAHGLPRR 588 Query: 594 DITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGL 653 EI R++ + NEGAR++EE IA + +D+V L+GYG+P +RGGP+ A G Sbjct: 589 THDAGEIQARLLAVLANEGARLVEEGIADSDAAVDMVKLHGYGFPRWRGGPLFAARQAGD 648 Query: 654 KHIAERLSAYAKAT 667 I L A A+ Sbjct: 649 ATIRAALDALDAAS 662 Lambda K H 0.317 0.134 0.383 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: 1180 Number of extensions: 66 Number of successful extensions: 6 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: 699 Length of database: 673 Length adjustment: 39 Effective length of query: 660 Effective length of database: 634 Effective search space: 418440 Effective search space used: 418440 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 (21.7 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