Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 3610445 Dshi_3826 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Dino:3610445 Length = 673 Score = 506 bits (1302), Expect = e-147 Identities = 294/663 (44%), Positives = 387/663 (58%), Gaps = 14/663 (2%) Query: 21 VTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPPVPP 80 VT+D+ PVNA S VR+GLL A+ + ++ AGR FIAG D+REF PP PP Sbjct: 18 VTVDNPPVNATSTAVRQGLLDAVTRV---QGARLAILRCAGRTFIAGGDMREFDAPPQPP 74 Query: 81 SLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGLLPGAG 140 LPDV + IEA P VA + G LGGGLE+A+ YRIA G + GLPEV +GL+PGAG Sbjct: 75 DLPDVVDAIEASATPFVAVMQGTVLGGGLEIAMGCAYRIAAPGTRFGLPEVTVGLIPGAG 134 Query: 141 GTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHELLAAHA 200 GTQR PRL G AA+D+ +G+ SA+EA A G +D + + A L + + Sbjct: 135 GTQRAPRLFGWDAAIDMACAGKLLSAQEAHARGALDAIADDPEAAARALVPEPRIPVSER 194 Query: 201 PVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDEGLRVE 260 P D+A ++ +LAA ++RG +PL+ +DA+ A PF EG R E Sbjct: 195 PAPPPPDSARIAAHRRTLAA----------RARGQTAPLQALDALLWATG-PFREGQRKE 243 Query: 261 RKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGVVGGGTMGAGIAVAVL 320 R L L S Q L HAFFAER V + R PR + I V+GGG MGAGIA A L Sbjct: 244 RALHLSLRASDQSRALRHAFFAERTVARPAVIRDRTPREIARIAVMGGGLMGAGIAAACL 303 Query: 321 DAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSYDALAGA 380 AG V ++ERD A+ R + + G + +G++ + A + A A Sbjct: 304 GAGYRVDLLERDAATAEAARDRVRGLIAGALRRGKIDQARHDAHCAALRTGVGIGHAAEA 363 Query: 381 DLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVIGLHFFS 440 DL IEAVFE+ A K+A FA L +V A+LATNTSYLD + + + P +GLHFF+ Sbjct: 364 DLAIEAVFEETATKRAAFAALAQVMAPDAILATNTSYLDPREIFAGIPAPDRCLGLHFFA 423 Query: 441 PANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYRSAADAM 500 PA++MKLLEVV + SA+ +ATAF LA +LRK V +G+CDGFIGNR+LA YR AA+ M Sbjct: 424 PAHVMKLLEVVRLPETSAETLATAFALAGRLRKVAVLSGICDGFIGNRMLAAYRRAAEYM 483 Query: 501 MEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQIADRLC 560 + DGA P QID A+RA+G MGPF+ DL+G I A R+R+ ATR RYV ++D+LC Sbjct: 484 LADGALPEQIDGAMRAYGMAMGPFEAQDLSGLHIAEANRRRQDATRPARERYVTLSDQLC 543 Query: 561 ERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIRRYMAAM 620 G GQ++G+G+Y Y EG R DP V A+I A G+ R+ EI R +A + Sbjct: 544 ALGRTGQRAGKGWYAYAEGDRRPRVDPAVTALITDYSAAHGLPRRTHDAGEIQARLLAVL 603 Query: 621 INEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIREFAKEDP 680 NEGA +V E IA VD+ L+GYGFPR+RGGP+ A G I A + P Sbjct: 604 ANEGARLVEEGIADSDAAVDMVKLHGYGFPRWRGGPLFAARQAGDATIRAALDALDAASP 663 Query: 681 LFW 683 W Sbjct: 664 GSW 666 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: 1146 Number of extensions: 49 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: 673 Length adjustment: 39 Effective length of query: 667 Effective length of database: 634 Effective search space: 422878 Effective search space used: 422878 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