Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 17892 b3846 fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (NCBI)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Keio:17892 Length = 729 Score = 347 bits (891), Expect = e-100 Identities = 232/674 (34%), Positives = 359/674 (53%), Gaps = 39/674 (5%) Query: 10 QDQVAIVTVDSP-PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68 +D +A + D+P VN L A + E + ++ ++L FI GADITEF Sbjct: 14 EDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITEF 73 Query: 69 GKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEA 119 P N V LE+ P PTIAA++G ALGGG E L +R+A + Sbjct: 74 LSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPDL 133 Query: 120 KLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENL 177 ++GLPE KLG++PG GG+ R+PR +G + A+++I G +GA +ALK GLV+ VV E L Sbjct: 134 RIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVKAEKL 193 Query: 178 VAGAVAFAKKVL---AEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKA-RGLEAPF 233 V GA A ++ + + + R+ + + KL+ +A S FT A + + A + AP Sbjct: 194 VEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMS-FTIAKGMVAQTAGKHYPAPI 252 Query: 234 ACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAF----FAEREAAKVDGVPDG 289 I AA EE L E + F+ L +++++A F + + +A K+ D Sbjct: 253 TAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVKGKAKKL--TKDV 310 Query: 290 TKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARG 349 P+ + A++GAG MGGGIA A G+PV + + ++ L G+ K RG Sbjct: 311 ETPK---QAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERG 367 Query: 350 GLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASN 409 + A ++ I + D+++EAV E VKK V + + VLASN Sbjct: 368 KIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVLASN 427 Query: 410 TSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKV 469 TS + I E+A +RP++ GMHFF+P + M L EI+RG K++ + + V+ A K+ K Sbjct: 428 TSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKMGKT 487 Query: 470 PVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLD 528 P+VV C GF NR+L +LL +GA +++D V+ K FG PMGP + D+ G+D Sbjct: 488 PIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYLLDVVGID 547 Query: 529 ----------IGWRSRKDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVE 578 G+ R + + I DAL +A RFGQK G G+++Y++ S+ P E + Sbjct: 548 TAHHAQAVMAAGFPQRMQKDYRDAI-DALFDANRFGQKNGLGFWRYKEDSKG-KPKKEED 605 Query: 579 TLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWP 638 + D LA++ +RD ++EEI+ RM+ PM+NE R LEE I A P++ D+ +YG G+P Sbjct: 606 AAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVYGLGFP 665 Query: 639 IYRGGPMHYADSVG 652 + GG + D++G Sbjct: 666 PFHGGAFRWLDTLG 679 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: 1045 Number of extensions: 52 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: 729 Length adjustment: 39 Effective length of query: 660 Effective length of database: 690 Effective search space: 455400 Effective search space used: 455400 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: 55 (25.8 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