Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_108402938.1 B9Z44_RS14295 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >NCBI__GCF_003063475.1:WP_108402938.1 Length = 682 Score = 484 bits (1247), Expect = e-141 Identities = 276/670 (41%), Positives = 384/670 (57%), Gaps = 15/670 (2%) Query: 10 VSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGAD 69 V +++ V ++T+D+ PVNA+S VRRGL++A+ + A AVL VG+ FIAGAD Sbjct: 7 VQGQVKQGVYVITLDNPPVNAISISVRRGLISAVNDFEQSNAQVAVL-VGSNGTFIAGAD 65 Query: 70 IREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLP 129 I EF + P L DV IE C KP+VAA+ GA LGGGLEVALA RIA +GLP Sbjct: 66 IHEFARTSDGPVLLDVVRVIENCKKPIVAALQGAVLGGGLEVALACDARIAHVDTVIGLP 125 Query: 130 EVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGL 189 EV LG++PGAGGTQ PR IG A+D+I + SA+EA L+D + SD ++A L Sbjct: 126 EVSLGIIPGAGGTQLLPRRIGISRAIDIICGAQRLSAEEAKHLRLVDSVVCSDILVAANL 185 Query: 190 --AYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEA 247 + + + D A + + R AK +D ++A Sbjct: 186 FARNIEHKSSVRDELVPNEDPALIDQAINRYTKLGRCRPAIAKA----------IDLIQA 235 Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVG 307 A P +EGL +E FLE S + L H FFAE+ K P+T+ P +NT+ V+G Sbjct: 236 AARLPIEEGLVLESAAFLELRKSQEAQALRHLFFAEKTCRKPPQTKEVAPIPINTVCVIG 295 Query: 308 GGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSR 367 GTMG GIA+ +LDA V ++E+D +L +G I Y + G+LS + + +S Sbjct: 296 AGTMGTGIAICLLDAEFSVMLLEQDKEALDKGEERIFSHYQKQVETGKLSPVEASKCLSH 355 Query: 368 WSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSV 427 S +++ LA ADLVIEAV+ED+ VKQ VF ++D+ A+LATNTSYL +D +A + Sbjct: 356 LLCSLNWEELAKADLVIEAVYEDMLVKQDVFKKIDQFANPNAILATNTSYLSVDKIALAT 415 Query: 428 SRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGN 487 +RP VIGLHFFSPAN+MKLLE+V KQ + + +L K PV GFIGN Sbjct: 416 TRPKRVIGLHFFSPANVMKLLEIVNAKQTCLETLHAVIAFGNRLNKYPVVTKDSFGFIGN 475 Query: 488 RVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRN 547 R+ YR+ + M+EDGA P ++DAA+ FG MGPF V DL+G DI W R R+ +N Sbjct: 476 RIYNAYRTQCEFMLEDGAWPEEVDAALVDFGMAMGPFTVADLSGLDIAW--RMRKTQRKN 533 Query: 548 PAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSF 607 RYV I D LCE G FG+K+ G+Y Y G + V II+ R I R+ Sbjct: 534 QETRYVDILDTLCELGRFGRKTSAGYYDYTNGKKQANTSELVRQIIENASQRRRIKRRTL 593 Query: 608 TDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPK 667 + I R + +M+NE A ++ E +A R D+DV F++GYGFPR++GGP+ +A + Sbjct: 594 NSKHIQNRALLSMVNEAALLMREGVAQRASDIDVVFVHGYGFPRWQGGPVFWARQQDRQQ 653 Query: 668 ILADIREFAK 677 + +DI A+ Sbjct: 654 LQSDIAGLAE 663 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: 918 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: 682 Length adjustment: 39 Effective length of query: 667 Effective length of database: 643 Effective search space: 428881 Effective search space used: 428881 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