Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_090275068.1 BLU11_RS15910 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >NCBI__GCF_900105005.1:WP_090275068.1 Length = 697 Score = 637 bits (1643), Expect = 0.0 Identities = 338/697 (48%), Positives = 459/697 (65%), Gaps = 2/697 (0%) Query: 7 ADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIA 66 +DVV+ E +G V ++ +++ PVNAL VR GL + AA+AD V+A+++V G FIA Sbjct: 2 SDVVTLERQGAVAVIRVNNPPVNALGVAVREGLQNSFNAAEADAQVKAIVLVCEGNTFIA 61 Query: 67 GADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKL 126 GADI+EFGKPP PSLPDV + IEA +KP +A IHG ALGGGLEVAL+ HYRIA AK+ Sbjct: 62 GADIKEFGKPPQAPSLPDVISGIEAGSKPSIAVIHGTALGGGLEVALSCHYRIARKDAKV 121 Query: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILA 186 GLPEV+LGLLPGAGGTQR PR++G ALD+I+SG A EA G++D L + +LA Sbjct: 122 GLPEVKLGLLPGAGGTQRLPRVVGVAKALDMIVSGTPIGAVEANELGVVDELFDGE-LLA 180 Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246 GL + +L+A RRT + + + AAVA RAE KK+ GLFSP + V AVE Sbjct: 181 AGLTFAEKLIAEGQGPRRTGERTDKLEGVDNAAAVAAKRAEIEKKTPGLFSPQRCVSAVE 240 Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGV 305 A+ P EGL+ ER+LF EC+ SPQRA L+HAFF ER K P R +N+ V Sbjct: 241 ASFTLPLAEGLKRERELFAECLVSPQRAALVHAFFTERLASKVDGLPKDTPVREINSAAV 300 Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365 +GGGTMG GIA+ +AG+PV ++E + + + Y + +G L+ M Sbjct: 301 IGGGTMGVGIAMCFANAGIPVKILEISEDARDKATQRARDTYGMSVKRGSLTEAALEKRM 360 Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425 + SG T Y L+ D+V+EAVFE++ VKQ VF LD CK GA+LA+NTS LD++ +A Sbjct: 361 ALVSGVTDYADLSDVDVVVEAVFEEMGVKQKVFEALDANCKPGAILASNTSSLDLNEIAR 420 Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485 RP DV+GLHFFSPAN+M+LLEVV ++ S DV+ATA + KKL+K V GVCDGF+ Sbjct: 421 FTKRPQDVVGLHFFSPANVMRLLEVVRGEKTSDDVLATAMAIGKKLKKVAVPVGVCDGFV 480 Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAAT 545 GNR++ Y ++ ++E+GA+P Q+DAA+R FG MG F + DL+G DIG A R R+ T Sbjct: 481 GNRMVFQYGRESEFLLEEGATPEQVDAALRKFGMAMGAFAMRDLSGLDIGLAIRTRQRQT 540 Query: 546 RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPR 605 + I D++ + G GQK+G+GFY+Y +GSR+ P+PE+ AI++A GI R Sbjct: 541 LPAEFKLPTILDKMAKAGMLGQKTGKGFYVYEKGSRAPLPNPELRAILEAASKEQGIERR 600 Query: 606 SFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGL 665 +D+ II R M A+INEGA ++ E +A R D+DV ++ GYGFP ++GGPM YAD VGL Sbjct: 601 ELSDDYIIERTMYALINEGAKILEEGVAQRASDIDVIYINGYGFPAHQGGPMFYADAVGL 660 Query: 666 PKILADIREFAKEDPLFWKPSPLLIELVERGADFASL 702 ++ A I EF ++ +WKP+PLL +L + G FA L Sbjct: 661 DRVYARICEFHEQLGAWWKPAPLLEKLAKEGRKFADL 697 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: 1131 Number of extensions: 36 Number of successful extensions: 3 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: 697 Length adjustment: 39 Effective length of query: 667 Effective length of database: 658 Effective search space: 438886 Effective search space used: 438886 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