Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Ga0059261_0837 Ga0059261_0837 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Korea:Ga0059261_0837 Length = 676 Score = 671 bits (1731), Expect = 0.0 Identities = 351/665 (52%), Positives = 453/665 (68%), Gaps = 11/665 (1%) Query: 1 MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60 M+ +T Q + ++T ++PPVNAL AAVR+G+ + D +++A V+ C GRTF Sbjct: 1 MTGPITTERQGDILVITSNNPPVNALGAAVRQGLDAAIKELAGDDSLKAAVIRCDGRTFF 60 Query: 61 AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120 AGADITEFGKP Q P+L ++ +E S KP +AA+HGTALGGG EVAL CH+R+AV AK Sbjct: 61 AGADITEFGKPMQEPSLPVLVDLIEASEKPVVAAVHGTALGGGCEVALACHYRIAVPSAK 120 Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLV 178 GLPEVKLG+LPGAGGTQRLPR G E A+++ G P+ A+ A GLV+ + ++L Sbjct: 121 FGLPEVKLGILPGAGGTQRLPRVGGVEFALELATKGDPVSASAAKDAGLVDRLAGEDSLT 180 Query: 179 AGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADA 238 A A+A+A ++ A RPL R + + A + TNA K+ R ++AP Sbjct: 181 ADAIAYANEIAAA-RPLPRTSEKPVTVEAGVFEAFRKTNA-----KRFRNMDAPAEIIAV 234 Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298 I P+ EG+++ER GFMKL++ QS A R+ FFAER+AAK+D VP+ TK RP+ RV Sbjct: 235 IEETAGKPYAEGVQRERMGFMKLIMGAQSAALRHIFFAERKAAKIDDVPEDTKLRPIKRV 294 Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAK 358 +IGAGTMGGGI+M+F +AGIPVT+ E +E L RG G ++KN+EATAA+G + + Sbjct: 295 GVIGAGTMGGGISMNFLSAGIPVTIAEMQQEALDRGTGTIRKNYEATAAKGRMTAEQVEG 354 Query: 359 RMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEI 418 M L+ + L ++ + DLIIEAV+E M VKK++F +D AKPGA+LASNTSYLSIDEI Sbjct: 355 AMGLLKSTLDLNDLAECDLIIEAVYENMDVKKDIFGKLDKIAKPGAILASNTSYLSIDEI 414 Query: 419 AATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDG 478 A+ T RP DV+GMHFFSPAN+MKL E+VRGAKT D L T + +AKKI KV VV GVC G Sbjct: 415 ASATGRPGDVVGMHFFSPANIMKLLEVVRGAKTDKDVLATVMDLAKKIKKVAVVAGVCYG 474 Query: 479 FVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRG 538 F+GNRML R ++ KLL EGA P QVD V +FGMPMGPF M DLAG+DIGW +D Sbjct: 475 FIGNRMLIPRQMEAMKLLHEGATPMQVDKVHVEFGMPMGPFQMSDLAGVDIGW--HRDPT 532 Query: 539 IKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDE 598 I DAL R+GQKT G+Y Y+ R P P P V +I + K G + ++TDE Sbjct: 533 RIENIRDALAAENRWGQKTKAGFYDYDD-KRNPSPSPRVAEIIEEFRTKTGTPQHEVTDE 591 Query: 599 EILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658 EI+ER Y M+NEGA+ILEE +A R SDIDVVW+YGYGWP YRGGPM +AD VGLK I Sbjct: 592 EIMERTFYTMVNEGAKILEEGMAQRASDIDVVWIYGYGWPPYRGGPMFWADQVGLKTIVA 651 Query: 659 RLSAY 663 L + Sbjct: 652 GLEKH 656 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: 1212 Number of extensions: 74 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: 676 Length adjustment: 39 Effective length of query: 660 Effective length of database: 637 Effective search space: 420420 Effective search space used: 420420 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