Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_013420474.1 RVAN_RS14570 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >NCBI__GCF_000166055.1:WP_013420474.1 Length = 695 Score = 594 bits (1531), Expect = e-174 Identities = 318/686 (46%), Positives = 438/686 (63%), Gaps = 7/686 (1%) Query: 10 VSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGAD 69 V+ E + V ++T+D+ P+N +S +VR GL+ AI A+AD +AV+++GAGRNF AGAD Sbjct: 6 VTYETKDGVGVITVDNPPLNVVSNEVRDGLMLAIRKAEADPVAKAVVLIGAGRNFAAGAD 65 Query: 70 IREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLP 129 I E P + D+C +E KPVVAA+HG + GLEVALA HYRIA A+LGLP Sbjct: 66 IYELTHPYSGADINDICAALEDLPKPVVAALHGTPVARGLEVALACHYRIAAKDARLGLP 125 Query: 130 EVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE-G 188 EV++GLLPG GGTQR PRL+GA+AALD+I+SG A +A GL+D + D + A Sbjct: 126 EVKVGLLPGGGGTQRLPRLVGAKAALDIIISGDLVPAVKAKTIGLVDEVVDGDILPAAIA 185 Query: 189 LAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAA 248 LA L+ H P R A DR + L R E ++ + + VDA+E+A Sbjct: 186 LAKSKSFLSKH-PKTRELSAKIAPDRGSHL--FEGRRDELRRRQPFQHAQFRCVDAIESA 242 Query: 249 IEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVVG 307 + PF +GL+ ER+LF E +D Q LIHAFFAERE K P R +PR + ++ VVG Sbjct: 243 VHLPFSQGLKRERELFNEALDDDQSKALIHAFFAEREAAKIPGFRTDVRPREIKSVAVVG 302 Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367 G MG GIA+A +AG PV +++RD A+L+RG A + K Y+ ++ +GRL +S Sbjct: 303 SGHMGGGIAMAFANAGFPVIVLDRDQAALSRGLAVVAKNYESMVRRGRLDQPGMNKRLSA 362 Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427 + +Y LA DLV+EA FED+ VK+ VF +LDR CK GA+ A+NTS LDID +AS Sbjct: 363 IRSTVNYKDLADVDLVVEAAFEDIGVKEQVFRDLDRACKKGAIFASNTSTLDIDEIASFT 422 Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487 RP DVIG HFFSPAN+ +L+EVV K+ SADV+ATA +AKK+ K V G CDGF GN Sbjct: 423 RRPGDVIGTHFFSPANVQRLVEVVRGKETSADVLATAMAVAKKIGKIGVAVGNCDGFAGN 482 Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRN 547 R+L Y + A ++E+GA+P ++D A+ +G MGPF V DL G D+ W R+RR Sbjct: 483 RMLEKYVTEAMIILEEGATPAEVDTALTRWGLAMGPFAVFDLTGIDVNWHIRQRRLKQGK 542 Query: 548 PAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSF 607 P + DR + G FGQK+G+GFY Y GSR+ PDPE +AII+A R G +S Sbjct: 543 PYGS--ALLDRFYDAGRFGQKTGKGFYRYETGSRAPLPDPEADAIIEAYRREVGPRVKSV 600 Query: 608 TDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPK 667 +++EI++R + A++NEGAN++ E + R D+D ++ GYGFP +RGGPMKYA++ GL + Sbjct: 601 SEQEIVKRTIYALVNEGANILDEGVVYRSGDIDTIYINGYGFPAWRGGPMKYAELRGLAE 660 Query: 668 ILADIREFAKEDPLFWKPSPLLIELV 693 +L+D+ F W+P+ LL LV Sbjct: 661 VLSDLDIFHMRFGDRWRPAALLKSLV 686 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: 1097 Number of extensions: 34 Number of successful extensions: 4 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: 695 Length adjustment: 39 Effective length of query: 667 Effective length of database: 656 Effective search space: 437552 Effective search space used: 437552 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