Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF3899 Psest_3969 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__psRCH2:GFF3899 Length = 412 Score = 355 bits (912), Expect = e-102 Identities = 184/400 (46%), Positives = 257/400 (64%), Gaps = 6/400 (1%) Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354 + A+IGAGTMG GI MS ANAG+ V ++ E L+R LG + + +G + Sbjct: 8 IQTAAVIGAGTMGRGIVMSLANAGVQVRWLDNNPEMLERALGTVADTYAHNVRQGRIDEA 67 Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414 A R A I+ + + D DL+IEAV+E + +K+++F +D KP +LASNTS L Sbjct: 68 QAAARRACISKAADYQALADVDLVIEAVYENLELKQKIFRELDGIVKPAGILASNTSALD 127 Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474 +D IAA TKRP+ V+G+HFFSPA++MKL EIVRGAKT+ L + + K++ KV V+ G Sbjct: 128 LDAIAAVTKRPEQVVGLHFFSPAHIMKLLEIVRGAKTSKAVLDASTELGKRMGKVSVIAG 187 Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR 534 C GF+GNRMLA +++ +L EGA P QVDA + FG MGPF M D+ G+D+ WR+R Sbjct: 188 NCQGFIGNRMLATYVREARMMLLEGAYPHQVDAALQGFGFAMGPFRMYDVVGIDLEWRAR 247 Query: 535 KDRG-----IKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLG 589 + G ++ ++ + LCE GRFGQK+ GYY+Y +GSR DPEV+ L+ +LG Sbjct: 248 ELAGKGQDEVEVQVDNRLCELGRFGQKSRMGYYRYAEGSRQAEHDPEVDALVQRESERLG 307 Query: 590 LKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYAD 649 +RR+I EEILER + ++NEGA+ILEE +A +DID V+LYGYG+P GGPM +AD Sbjct: 308 FQRREIGSEEILERCLLALVNEGAKILEEGMAESSADIDTVYLYGYGFPAEVGGPMTWAD 367 Query: 650 SVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFA 689 GL I +RL+A A+ + +PA L+ LA G FA Sbjct: 368 RQGLPAIRDRLNALAE-RHGAHWQPAELIDSLATLGGRFA 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: 617 Number of extensions: 26 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: 412 Length adjustment: 35 Effective length of query: 664 Effective length of database: 377 Effective search space: 250328 Effective search space used: 250328 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