Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate H281DRAFT_00756 H281DRAFT_00756 Enoyl-CoA hydratase/carnithine racemase
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >FitnessBrowser__Burk376:H281DRAFT_00756 Length = 376 Score = 283 bits (724), Expect = 6e-81 Identities = 166/370 (44%), Positives = 224/370 (60%), Gaps = 10/370 (2%) Query: 14 AAAPSADDEVRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRG 73 +A P A DEV N IG I L RP+ LNALS MI + A L W D+ AVV+R Sbjct: 4 SALPEASDEVATYVANCIGFIELERPKALNALSLGMIRAIHAALDDWRENPDVLAVVVRS 63 Query: 74 AGPKAFCAGGDIRALYDSFHAGTALHRQ-FFVDEYQLDYRLHCYPKPVVALMDGIVMGGG 132 P+AFCAGGDIR LY+S G R FF++EY+L++ + YPKP +AL +G+VMGGG Sbjct: 64 QHPRAFCAGGDIRFLYESAKRGEHEARDAFFIEEYRLNHAIFTYPKPYIALTNGVVMGGG 123 Query: 133 MGLAQAAH----LRVLTERSRVAMPETGIGLVPDVGASHFLSKLPLALALYVGLTGVTLG 188 MG++Q AH LRV+T+ +++AMPET IGL PDVGAS FL++ P A+ Y+ +TG +G Sbjct: 124 MGISQGAHRTGGLRVVTQSTKMAMPETRIGLFPDVGASWFLARTPGAIGRYLAVTGEAIG 183 Query: 189 AADTLLCKLADIAVPAASLEHFEQTLAA--INRTGDVLADLRAALQATPDAGE-QAAPLQ 245 AAD L LAD+ + A+L L + R DV+A + +A A + + +PL Sbjct: 184 AADALYAGLADLYIDDAALPALIDILRSELFERGADVVACVERESRAYQVAPQPEQSPLA 243 Query: 246 SVLPAVLRHFRADASVAGLLDSLAAESDPAYADWAARTLDILRGRSPLMMAVTRELLLRG 305 + RHF A V +L SL + D ADWA +T+ +LR RSPL MAV+ E++ R Sbjct: 244 RARRLIDRHF-ALPDVPRILASLQQKCDRDTADWAEQTIAVLRERSPLSMAVSLEVVTRA 302 Query: 306 RDLDLADCFRMELGVVSHAFSQGDFIEGVRALIVDKDNAPRWRVKDASEVSEAVVQSFFD 365 +A+ R +L + +F QGD +EG+RA I+DKDNAP WR +VS A V F+ Sbjct: 303 EG-SMAEVLRGDLDLTRSSFLQGDAVEGIRARIIDKDNAPHWRFARIEDVSAADVAKMFE 361 Query: 366 SPWPREPHPL 375 SPWP HPL Sbjct: 362 SPWPAYEHPL 371 Lambda K H 0.322 0.137 0.405 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: 361 Number of extensions: 19 Number of successful extensions: 5 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: 384 Length of database: 376 Length adjustment: 30 Effective length of query: 354 Effective length of database: 346 Effective search space: 122484 Effective search space used: 122484 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 (21.9 bits) S2: 50 (23.9 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