Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_023433142.1 N177_RS14610 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >NCBI__GCF_000496075.1:WP_023433142.1 Length = 688 Score = 458 bits (1179), Expect = e-133 Identities = 269/678 (39%), Positives = 381/678 (56%), Gaps = 15/678 (2%) Query: 26 APVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPPVPPSLPDV 85 APV ADVR L+ + AA V A+++ + + GAD E + P+L D+ Sbjct: 25 APV--FGADVRAALIGGLRAALLRPDVRAIVLAIPEGSAMMGADEGEIEEACKAPTLMDL 82 Query: 86 CNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGLLPGAGGTQRT 145 +E KPVVAA+ G+ LG G E ALA H R+A A+LGLP + G++P G QR Sbjct: 83 QAEVEDAAKPVVAALSGSVLGAGFEFALACHGRVASKTARLGLPHAKFGMMPLGGAIQRL 142 Query: 146 PRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHELLAAHAPVRRT 205 RL G + LD++LSG A A G++D + DD+ A A+ H + RR Sbjct: 143 SRLAGIRVTLDMVLSGTAIDAAAAEEAGIVDWV-VEDDLTAAASAFAHCIAEGEQASRRA 201 Query: 206 RDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDEGLRVERKLFL 265 D + DR ++ A +K RG + A+ A E PFDEGL E +L L Sbjct: 202 GDLD-VPDRDEKQDILSGAIRTHGRKLRGTRQLELTLSALRVAAETPFDEGLATETELSL 260 Query: 266 ECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVVGGGTMGAGIAVAVLDAGL 324 E + + H AERE + P+ A + + +G+VG GTMG GIA+ L+ GL Sbjct: 261 ELARGAEASARRHVARAERETWRIPDIPAETETLPVERVGIVGAGTMGGGIAMNFLNTGL 320 Query: 325 PVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSYDALAGADLVI 384 PVT++E +L RG + I + YDG KGR+S + M +G+ + + LA DLVI Sbjct: 321 PVTIVETRQEALDRGVSVIRRNYDGSARKGRMSQDDVEVRMRLLTGTLALEDLASCDLVI 380 Query: 385 EAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVIGLHFFSPANI 444 EAVFE++ VK+ +F LD + + A+LA+NTSYLD+D +A + SRP V+GLHFFSPANI Sbjct: 381 EAVFENMEVKKEIFGRLDAIVRPDAILASNTSYLDVDEIARATSRPERVLGLHFFSPANI 440 Query: 445 MKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYRSAADAMMEDG 504 M+LLEVV ++ S V+AT +LA+++ K V GVC GF+GNR+LA + A ++ +G Sbjct: 441 MRLLEVVRAEKTSKPVLATTMQLARRIGKVGVMVGVCFGFVGNRMLAQRQREATKLILEG 500 Query: 505 ASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQIADRLCERGW 564 A P+ +D + FG PMGPF + DLAG D+GW+ + T + + LCE Sbjct: 501 AMPWDVDRVLYDFGLPMGPFAMSDLAGLDLGWSRETSKGET---------VKEILCEMDR 551 Query: 565 FGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIRRYMAAMINEG 624 GQK+G GFY Y E +R P E +I R G+ R DEEI++R + MINEG Sbjct: 552 RGQKTGAGFYDYDE-NRKAVPSKVTETVILDLAERRGMARREIADEEILKRCIYPMINEG 610 Query: 625 ANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIREFAKEDPLFWK 684 A ++ E A+R D+DV ++ GYG+P +RGGPM Y D +GL ++L +R F ++ Sbjct: 611 AKILDEGKAIRASDIDVVWINGYGWPAHRGGPMYYGDRIGLDEVLETMRRFEATQGEDFR 670 Query: 685 PSPLLIELVERGADFASL 702 P+PLL LV G F L Sbjct: 671 PAPLLERLVREGRGFGDL 688 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: 1031 Number of extensions: 50 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 706 Length of database: 688 Length adjustment: 39 Effective length of query: 667 Effective length of database: 649 Effective search space: 432883 Effective search space used: 432883 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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