Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate SM_b21632 SM_b21632 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::BFirm:BPHYT_RS13545 (706 letters) >FitnessBrowser__Smeli:SM_b21632 Length = 438 Score = 351 bits (900), Expect = e-101 Identities = 195/425 (45%), Positives = 267/425 (62%), Gaps = 11/425 (2%) Query: 276 LIHAFFAEREVLKAPETRAAKPRTLNTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDAS 335 L + F AER P +PR + + V+GGGTMG GIA A+L AGLP+ ++ERD+A+ Sbjct: 20 LRYVFHAERAARHPPALAGIEPRPIRSAAVIGGGTMGTGIAAALLHAGLPLVLVERDEAA 79 Query: 336 LARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQ 395 + R A + ++DG + +GR+SA A ++ +GST Y A+A ADL+IEAVFEDL VK+ Sbjct: 80 VERALARLRTIFDGAVKRGRISAGLAAERLAGVTGSTDYTAIAEADLIIEAVFEDLDVKR 139 Query: 396 AVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQ 455 VF L VC+A A+LATNTSYLD + +A+ + +GLHFFSPA +MKLLE+V + Sbjct: 140 DVFRRLAAVCRADAILATNTSYLDPERIAADIGSRERFLGLHFFSPAQVMKLLEIVPTQA 199 Query: 456 VSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVR 515 + DV+AT F LA+ L K PVRAG+ DGFIGNR+L V R+ A+ ++ GA+P +DAA+R Sbjct: 200 TAPDVLATGFALARMLNKIPVRAGISDGFIGNRILKVTRAQAERLLLSGATPAAVDAAMR 259 Query: 516 AFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQIADRLCERGWFGQKSGRGFYL 575 AFG PMGPF+ DL G DI AA +RRAA + +ADRL FGQKSG G+Y Sbjct: 260 AFGLPMGPFEAQDLGGLDI--AAFQRRAARARGETTFAPVADRLSAIERFGQKSGGGWYD 317 Query: 576 YPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIRRYMAAMINEGANVVHERIALR 635 Y G R+ P V II AE AR G R + + I+ + M+NE A ++ + ALR Sbjct: 318 YAPGDRTPRPSATVARII-AEEAR-GWPRRDWDEASIVGCILWPMVNEAARILEDGTALR 375 Query: 636 PLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKI---LADIREFAKEDPLFWKPSPLLIEL 692 D+D+ ++GYGFPR+RGG M +A+ GL K+ L+ + E DP P L+ Sbjct: 376 ASDIDLVEIHGYGFPRWRGGLMHHAEAHGLHKVAGALSGLAEAGLADP----PCDPLLRA 431 Query: 693 VERGA 697 RG+ Sbjct: 432 ASRGS 436 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: 764 Number of extensions: 30 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: 438 Length adjustment: 36 Effective length of query: 670 Effective length of database: 402 Effective search space: 269340 Effective search space used: 269340 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: 53 (25.0 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