Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Ga0059261_2827 Ga0059261_2827 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Korea:Ga0059261_2827 Length = 683 Score = 597 bits (1538), Expect = e-175 Identities = 320/692 (46%), Positives = 445/692 (64%), Gaps = 17/692 (2%) Query: 1 MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60 ++E + +D VAIVT+D PPVNA+S A+ G+ + + AA++D A +AIVL+CAGRTFI Sbjct: 4 INEGTSLTVEDGVAIVTLDFPPVNAMSPALMDGLYDALMAALSDDAAKAIVLICAGRTFI 63 Query: 61 AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120 AGAD+ GK + ++ENSPKPT+AA+HGTALGGG+E AL H+R+AV A+ Sbjct: 64 AGADLKSLGKVQPKVDFFALQDSIENSPKPTVAALHGTALGGGMETALTFHYRIAVPSAR 123 Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN--LV 178 +GLPEV LGLLPG GGTQRLPR G E A+ +++ G +GA EAL GL++ + L Sbjct: 124 MGLPEVNLGLLPGGGGTQRLPRITGAEAALDLLISGRQVGAKEALTIGLIDRLAAEGALR 183 Query: 179 AGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADA 238 A+AFAK+++ P +R+RD ++K+AA + D ++F + K+ GL+AP A Sbjct: 184 EDAIAFAKELVDAGEPPKRIRDCEAKVAADRKDANLFERFRTSHAKQLNGLDAPQAIVRC 243 Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298 + AA+ P+E+GL ER F L+ QS A R+ F AER A K+ G+ PV++V Sbjct: 244 VEAAVAGPWEKGLAIERTEFQTLLAGPQSAALRHVFMAERAAQKIPGLRADLPLIPVTKV 303 Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAK 358 I+GAGTMG GIAM+F AG VT++ET + L RG+ + ++ RG L D Sbjct: 304 GIVGAGTMGSGIAMAFLAAGFAVTVVETQQAALDRGVAHITATLQSRVERGKLAADKAEA 363 Query: 359 RMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEI 418 ++A +T + L + DADL++EA+FE +A K+ +F + A +P +LA+NTS+L +D I Sbjct: 364 QIAALTPTLDLSALADADLVVEAIFENLAAKQALFGTLSAIVRPDTILATNTSFLDVDAI 423 Query: 419 AATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDG 478 AA P+ VLGMHFFSPANVM+L E+VR AKT+ L + +++AKK+ K VV GVC G Sbjct: 424 AAGAAGPERVLGMHFFSPANVMRLLEVVRAAKTSEAVLASVMALAKKLGKAAVVSGVCFG 483 Query: 479 FVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRG 538 F+GNRMLAAR ++ ++ G LP +D ++T FG PMGPFAM DLAGLDIGW D Sbjct: 484 FIGNRMLAARQVHADAMVLAGVLPWNIDRILTGFGFPMGPFAMLDLAGLDIGWEGDTD-- 541 Query: 539 IKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDE 598 + L AGR GQK+G GYY YE ++ P P +I LA + ++D Sbjct: 542 ---SVKSRLVAAGRKGQKSGAGYYDYE--NKTPSPSQTALDVIAG-LASVAPGSVTLSDR 595 Query: 599 EILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658 EIL+R++ PMINEGA+ILEE IA R SDID+VW+ GYGWP GGPM +AD++GL + + Sbjct: 596 EILDRLLLPMINEGAKILEEGIALRGSDIDLVWITGYGWPAQTGGPMFHADAIGLTRVVD 655 Query: 659 RLSAYAKATNDPSLEPAPLLARLAAEGKTFAS 690 L +EPA LL +LA+EG + A+ Sbjct: 656 GL-------RHMGVEPAALLLKLASEGGSLAA 680 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: 1111 Number of extensions: 43 Number of successful extensions: 5 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: 683 Length adjustment: 39 Effective length of query: 660 Effective length of database: 644 Effective search space: 425040 Effective search space used: 425040 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