Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__PV4:5210423 Length = 708 Score = 545 bits (1403), Expect = e-159 Identities = 302/700 (43%), Positives = 434/700 (62%), Gaps = 15/700 (2%) Query: 13 ELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIRE 72 ++ G+ ++ ++ PVN+L +R LLA ++ A+AD++V+A+++ +G+ F GADI E Sbjct: 8 QIHGRTAVIILNQPPVNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISE 67 Query: 73 FGKPPV--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPE 130 F P+LP VC+ +EA K VVAA++G ALGGG E+ LA YRIA+ AKLGLPE Sbjct: 68 FSSDDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPE 127 Query: 131 VQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRL-GSSDDILAEGL 189 V LG+LPGAGGTQR PR+ G Q AL++I SGR A L G+ID L + + + Sbjct: 128 VNLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNLYQDGGNFIQAAV 187 Query: 190 AYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAI 249 + EL+A H P R + + + +S RA A++SRG ++P + + AVEAA Sbjct: 188 DFAQELVAQHKPKRSCFEMSVDTSNISS-EIFNEFRAAIARRSRGYYAPERCIQAVEAAC 246 Query: 250 EQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAP--ETRAAKPRTLNTIGVVG 307 E P EGL+ E +LF+EC+D+PQ H FFAER V K P + R + + V+G Sbjct: 247 ELPLAEGLKREHQLFMECLDTPQARAQQHLFFAERGVAKIPGINPKTTATREIRKVAVIG 306 Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367 GTMG GIA+ ++ G+P +++ + +L RG I K Y+ + KG+LS + M+ Sbjct: 307 SGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQAQLDERMAL 366 Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427 SG+T Y +A DLVIEAVFE + +K+ VF LD CK GA+LATNTS LD+D +A+ Sbjct: 367 LSGTTDYADIADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLDVDEIAAET 426 Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487 SRP DV+GLHFFSPAN+M+LLE+V + + D + T +LA++++K PV +GVC GFIGN Sbjct: 427 SRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSGVCWGFIGN 486 Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARK-RRAATR 546 R Y + +++ +GASP QID FG PMG +VDLAG D+G R+ R+A T Sbjct: 487 RATDSYLRESMSLILEGASPAQIDKVHTEFGMPMGLPSMVDLAGIDVGILTREDRKAFTT 546 Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGIT--- 603 + + I +L + +GQK+GRG Y+Y EG R DPEV + G+T Sbjct: 547 DLDPSHFAILHKLYAKQRYGQKTGRGLYIY-EG-RDKQEDPEVLELAAEAAKEFGVTRRS 604 Query: 604 PRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMV 663 P +D+EI+ R + +INEGA ++ E IALR D+D+ YG+GFP +RGGPM+YAD + Sbjct: 605 PEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFPIFRGGPMQYADEI 664 Query: 664 GLPKILADI---REFAKEDPLFWKPSPLLIELVERGADFA 700 GL ++L + R+ + L++KP+PLL LV+ G FA Sbjct: 665 GLERVLTALNKYRDTLDKGELWFKPAPLLERLVKEGKTFA 704 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: 1086 Number of extensions: 49 Number of successful extensions: 7 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: 708 Length adjustment: 39 Effective length of query: 667 Effective length of database: 669 Effective search space: 446223 Effective search space used: 446223 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: 55 (25.8 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