Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate H281DRAFT_00361 H281DRAFT_00361 short chain enoyl-CoA hydratase /3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Burk376:H281DRAFT_00361 Length = 706 Score = 1280 bits (3311), Expect = 0.0 Identities = 648/705 (91%), Positives = 682/705 (96%) Query: 1 MTPNPSADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGA 60 M+ S DVV+RELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAAD+D +V+AVLIVGA Sbjct: 1 MSLTTSTDVVTRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADSDPSVQAVLIVGA 60 Query: 61 GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIA 120 GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYR+A Sbjct: 61 GRNFIAGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRLA 120 Query: 121 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGS 180 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDL+LSGRHA+A+EALA GL+DRLGS Sbjct: 121 VDGAKLGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLMLSGRHANAQEALALGLVDRLGS 180 Query: 181 SDDILAEGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLK 240 SDDILAEGLAYVHELLA HAPVRRTRDA AL+DRA+SLAAVATARAETAKKSRGLFSPLK Sbjct: 181 SDDILAEGLAYVHELLAGHAPVRRTRDATALNDRASSLAAVATARAETAKKSRGLFSPLK 240 Query: 241 IVDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTL 300 IVDAVEAAI QPF++GLR ER+LFLEC+DSPQRAGL+HAFFAEREVLKAPETR KPR L Sbjct: 241 IVDAVEAAIAQPFEDGLRRERQLFLECLDSPQRAGLVHAFFAEREVLKAPETRDTKPRAL 300 Query: 301 NTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEK 360 N IGVVGGGTMGAGIAVAVLDAGLPVTMIERD+ASLARGRAHIEKVYDGLIAKGR+SAEK Sbjct: 301 NAIGVVGGGTMGAGIAVAVLDAGLPVTMIERDEASLARGRAHIEKVYDGLIAKGRMSAEK 360 Query: 361 KAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDI 420 KA LM+RW+GSTSYDALA ADLVIEAVFEDL+VKQAVFAELDRVCK GAVLATNTSYLDI Sbjct: 361 KAQLMARWTGSTSYDALADADLVIEAVFEDLSVKQAVFAELDRVCKPGAVLATNTSYLDI 420 Query: 421 DALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGV 480 DA+A+S+SRPADVIGLHFFSPANIMKLLEVVVPK VSADVVATAFELAKKLRKTPVRAGV Sbjct: 421 DAIAASISRPADVIGLHFFSPANIMKLLEVVVPKAVSADVVATAFELAKKLRKTPVRAGV 480 Query: 481 CDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540 CDGFIGNR+LAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK Sbjct: 481 CDGFIGNRILAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK 540 Query: 541 RRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARA 600 RRAATRNPAARYVQIADRLCERGWFGQK+GRGFYLYPEGSRSG PDPEVEAIIDAER RA Sbjct: 541 RRAATRNPAARYVQIADRLCERGWFGQKTGRGFYLYPEGSRSGQPDPEVEAIIDAERVRA 600 Query: 601 GITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660 GITPR F+D+EIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA Sbjct: 601 GITPREFSDDEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYA 660 Query: 661 DMVGLPKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQS 705 DM+GLP+ILADIREFAKEDPLFW+ SPLLI+LVERGADFASLN + Sbjct: 661 DMIGLPRILADIREFAKEDPLFWRASPLLIDLVERGADFASLNHA 705 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: 1536 Number of extensions: 52 Number of successful extensions: 1 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: 706 Length adjustment: 39 Effective length of query: 667 Effective length of database: 667 Effective search space: 444889 Effective search space used: 444889 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 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