Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Pf6N2E2_3894 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3894 Length = 408 Score = 342 bits (878), Expect = 2e-98 Identities = 183/403 (45%), Positives = 253/403 (62%), Gaps = 6/403 (1%) Query: 292 PRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGL 351 P + R A++GAGTMG GI M ANAG+ V ++ + L++ L + + + +G + Sbjct: 5 PFDIQRAAVVGAGTMGRGIVMCLANAGVAVQWVDNNPQMLEQALVAVAETYAHGVRQGRI 64 Query: 352 PPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTS 411 R+A +T +++ DL+IEAV+E + +K+ +F +D KP A+LASNTS Sbjct: 65 DQGEADARIARVTRADDYAAIRNVDLVIEAVYENLELKRRIFRELDGLLKPAAILASNTS 124 Query: 412 YLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPV 471 L ID IAA T+RP VLG+HFFSPA++MKL E+VRGA+T+ L A+ + K++ KV V Sbjct: 125 ALDIDAIAAVTRRPTQVLGLHFFSPAHIMKLLEVVRGAQTSKAVLDAALVLGKRMGKVSV 184 Query: 472 VVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGW 531 V G C GF+GNRML ++ K+L EGA P QVDA + FG MGPF M D+ G+D+ W Sbjct: 185 VSGNCHGFIGNRMLHPYVLEARKMLLEGAFPHQVDAALQGFGFAMGPFRMYDVVGIDLEW 244 Query: 532 RSRKDRGI-----KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLA 586 R+R+ G + ++ + LCE GRFGQK+G GYY YE GSR D EV+ L+ Sbjct: 245 RARELAGTGQDAPEVQVDNRLCELGRFGQKSGNGYYHYEPGSRQAEHDVEVDALVLRVSE 304 Query: 587 KLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMH 646 LG +RR+I +EILER + ++NEGA+ILEE IA DID V+L GYG+P +GGPM Sbjct: 305 ALGFQRREIGPQEILERCLLALVNEGAKILEEGIAESAQDIDRVYLNGYGFPADKGGPMA 364 Query: 647 YADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFA 689 +AD GL+ I RL A D +PA L+ LAA+GK FA Sbjct: 365 WADGQGLEDIHARLLALETKQGD-QWKPARLIGDLAAQGKGFA 406 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: 614 Number of extensions: 25 Number of successful extensions: 2 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: 408 Length adjustment: 35 Effective length of query: 664 Effective length of database: 373 Effective search space: 247672 Effective search space used: 247672 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: 52 (24.6 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