Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__PV4:5210423 Length = 708 Score = 629 bits (1623), Expect = 0.0 Identities = 346/708 (48%), Positives = 468/708 (66%), Gaps = 27/708 (3%) Query: 5 VTRATQDQV----AIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60 +T AT Q+ A++ ++ PPVN+L A+R +L ++ A AD +V AIVL +G+ F Sbjct: 1 MTNATLYQIHGRTAVIILNQPPVNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFC 60 Query: 61 AGADITEFGKPPQ--PPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKE 118 GADI+EF P L V ALE SPK +AA++G ALGGG E+ L C +R+A+ Sbjct: 61 GGADISEFSSDDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPA 120 Query: 119 AKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE--- 175 AKLGLPEV LG+LPGAGGTQRLPR G +LA++MI G P+GAA L G+++ + + Sbjct: 121 AKLGLPEVNLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNLYQDGG 180 Query: 176 NLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFAC 235 N + AV FA++++A+ +P R + + + IF AA+ +++RG AP C Sbjct: 181 NFIQAAVDFAQELVAQHKPKRSCFE--MSVDTSNISSEIFNEFRAAIARRSRGYYAPERC 238 Query: 236 ADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGV-PDGTKPRP 294 A+ AA +LP EGLK+E + FM+ + + Q++AQ++ FFAER AK+ G+ P T R Sbjct: 239 IQAVEAACELPLAEGLKREHQLFMECLDTPQARAQQHLFFAERGVAKIPGINPKTTATRE 298 Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354 + +VA+IG+GTMGGGIAM+F N GIP +++ E L+RGLG+++KN+E T +G L Sbjct: 299 IRKVAVIGSGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQA 358 Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414 +RMAL++G ++ D DL+IEAVFE M +KK+VF +DA KPGA+LA+NTS L Sbjct: 359 QLDERMALLSGTTDYADIADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLD 418 Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474 +DEIAA T RPQDVLG+HFFSPANVM+L EIVR KTAPDALLT V +A++I KVPVV G Sbjct: 419 VDEIAAETSRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSG 478 Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR 534 VC GF+GNR + ++S L+ EGA P Q+D V T+FGMPMG +M DLAG+D+G +R Sbjct: 479 VCWGFIGNRATDSYLRESMSLILEGASPAQIDKVHTEFGMPMGLPSMVDLAGIDVGILTR 538 Query: 535 KDRGIKS--------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLA 586 +DR + I L R+GQKTG+G Y YE R DPEV L + Sbjct: 539 EDRKAFTTDLDPSHFAILHKLYAKQRYGQKTGRGLYIYE--GRDKQEDPEVLELAAEAAK 596 Query: 587 KLGLKRR---DITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGG 643 + G+ RR I+D+EILER +YP+INEGARILEE IA R SDID+V YG+G+PI+RGG Sbjct: 597 EFGVTRRSPEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFPIFRGG 656 Query: 644 PMHYADSVGLKHIAERLSAYAKATNDPSL--EPAPLLARLAAEGKTFA 689 PM YAD +GL+ + L+ Y + L +PAPLL RL EGKTFA Sbjct: 657 PMQYADEIGLERVLTALNKYRDTLDKGELWFKPAPLLERLVKEGKTFA 704 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: 1089 Number of extensions: 57 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: 708 Length adjustment: 39 Effective length of query: 660 Effective length of database: 669 Effective search space: 441540 Effective search space used: 441540 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