Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate PP_2047 PP_2047 3-hydroxyacyl-CoA dehydrogenase family protein
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Putida:PP_2047 Length = 412 Score = 312 bits (800), Expect = 2e-89 Identities = 169/403 (41%), Positives = 244/403 (60%), Gaps = 2/403 (0%) Query: 297 PRTLNTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRL 356 P +N + V+G GTMG GI +++ +AGL V ++ + A+L G + + + + K R+ Sbjct: 4 PFPINQVAVIGAGTMGRGIVISLANAGLSVLWLDCNAAALEAGLGMVSQAWAQQVDKQRI 63 Query: 357 SAEKKAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTS 416 + + A ++R Y ALA ADLVIEAV+E+LA+KQ +F LD K A+LA+NTS Sbjct: 64 TQAQADACLARVQAVDGYPALAEADLVIEAVYENLALKQEIFCALDAHLKPRAILASNTS 123 Query: 417 YLDIDALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPV 476 LDIDA+A+ RP+ V+GLHFFSPA++MKLLE+V V+ A L +++ K + Sbjct: 124 ALDIDAIAAVTQRPSQVLGLHFFSPAHVMKLLEIVRGTHTDQKVLDAAKALGERMGKVAI 183 Query: 477 RAGVCDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGW 536 AG C GFIGNR+L Y A ++ +GA P+Q+DA ++ FGF MGPF++ D+ G D+ W Sbjct: 184 VAGNCPGFIGNRMLRSYVGEARKLLLEGALPHQVDAVLQQFGFAMGPFRMYDVVGIDLEW 243 Query: 537 AARKRRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAE 596 R R+ A + VQ+ + LCE G GQK+G+G+Y Y GSR DP+V+A++ Sbjct: 244 --RARQLAGQGMHDPLVQVDNALCELGRLGQKTGQGYYRYAPGSRQAEHDPQVDALVLQV 301 Query: 597 RARAGITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGP 656 G R + EEI+ R + A++NEGA V+ E IA D+D +L+GYGFP GGP Sbjct: 302 SQNLGYRRRGISAEEILERCLLALVNEGAKVLQEGIAASSGDIDQVWLHGYGFPAATGGP 361 Query: 657 MKYADMVGLPKILADIREFAKEDPLFWKPSPLLIELVERGADF 699 M++AD G P ILA + W+P+ LL LV G F Sbjct: 362 MRWADEQGAPFILARLEYLQGVLGEHWRPAGLLYSLVAGGKRF 404 Lambda K H 0.320 0.136 0.392 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: 611 Number of extensions: 27 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: 706 Length of database: 412 Length adjustment: 35 Effective length of query: 671 Effective length of database: 377 Effective search space: 252967 Effective search space used: 252967 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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