Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate RR42_RS35270 RR42_RS35270 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Cup4G11:RR42_RS35270 Length = 693 Score = 719 bits (1855), Expect = 0.0 Identities = 374/693 (53%), Positives = 492/693 (70%), Gaps = 6/693 (0%) Query: 1 MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60 ++ V A + ++AI+T++SPPVNALSAAVR GIL + A+AD V+ IVL CAG+TFI Sbjct: 4 INAVADLAVEGEIAILTLNSPPVNALSAAVRAGILAGIERAIADSNVRGIVLTCAGKTFI 63 Query: 61 AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120 AGADITEFGKPP P+L DV AA+E SPKP +AAIHGTALGGGLEVAL CH+RVA + A+ Sbjct: 64 AGADITEFGKPPVGPSLADVQAAIEGSPKPVVAAIHGTALGGGLEVALVCHYRVAARSAR 123 Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN--LV 178 GLPEV LGLLPGAGGTQRLPR VGP A+ M+ G+ IGAA A + GL + V E+ L Sbjct: 124 CGLPEVNLGLLPGAGGTQRLPRIVGPAKALDMVTSGAHIGAAAAAEMGLFDLVTEDAALR 183 Query: 179 AGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADA 238 A A+AFA++V AE+RPLR++RD + K+ AA+ +F + A +K RG +AP Sbjct: 184 ASAIAFARQVNAEQRPLRKVRDLNEKVEAARGKPELFADFRRANARKFRGFDAPEYNIRC 243 Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298 I AA++LPF+EG+K ER+ F++L+ QS AQRY FFA R+ V VP T V +V Sbjct: 244 IEAAVNLPFDEGMKVERKLFLELMNGTQSAAQRYYFFASRQVWNVPDVPADTPVIDVKKV 303 Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAK 358 IIGAGTMGGGIAM+ NAGIPV ++ET ++ L RG+ ++ N++ TA +G + + Sbjct: 304 GIIGAGTMGGGIAMNMLNAGIPVVIVETAQQALDRGVRTIRANYDNTAKKGRITAADVDR 363 Query: 359 RMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEI 418 RMAL+T + L + DADL+IEAV+E M VKK++F +D KPGA+LA+NTS L ++EI Sbjct: 364 RMALLTPTLELGQLADADLVIEAVYENMDVKKDIFGKLDKIVKPGAILATNTSALDVNEI 423 Query: 419 AATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDG 478 A T RP+ V+G+HFFSPANVMKL E+VRG KTA + T++ +A+KI K+ +VGVC G Sbjct: 424 ARATSRPESVIGLHFFSPANVMKLLEVVRGDKTAKPVIRTSMELARKIGKIAALVGVCPG 483 Query: 479 FVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRG 538 FVGNRMLA R ++++KL+ EGALP +D V+ FG PMGPFAM DLAGLD+GW +++ Sbjct: 484 FVGNRMLAQRQREAQKLVLEGALPWDIDRVLYNFGFPMGPFAMSDLAGLDLGW--IREKS 541 Query: 539 IKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDE 598 + + + LCE R GQKTG GYY Y++ R +P P VE +I D A+ G R + ++ Sbjct: 542 SSATLREILCEMDRRGQKTGAGYYDYDE-KRNAIPSPVVEGIIRDFAARQGKTSRVVCEQ 600 Query: 599 EILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658 EILER +YPMINEGA+ILEE A R SDIDVVW+ GYGWP+YRGGPM YAD++GL + Sbjct: 601 EILERCIYPMINEGAKILEEGKAIRASDIDVVWVNGYGWPVYRGGPMCYADTIGLDKVLA 660 Query: 659 RLSAYAKATNDPSLEPAPLLARLAAEGKTFASL 691 + + +AT +PA LL L A+GK F+ L Sbjct: 661 VMKNF-EATLGADFKPARLLEDLVAQGKKFSDL 692 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: 1122 Number of extensions: 58 Number of successful extensions: 4 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: 693 Length adjustment: 39 Effective length of query: 660 Effective length of database: 654 Effective search space: 431640 Effective search space used: 431640 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