Align 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized)
to candidate CCNA_01414 CCNA_01414 3-hydroxyisobutyryl-CoA hydrolase
Query= SwissProt::Q5XIE6 (385 letters) >FitnessBrowser__Caulo:CCNA_01414 Length = 350 Score = 272 bits (696), Expect = 9e-78 Identities = 147/348 (42%), Positives = 213/348 (61%), Gaps = 10/348 (2%) Query: 32 TETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGK 91 T+ EVL+ G ITLNRPK L+AL+L M + L W+ DP+ ++++I G + Sbjct: 2 TDDPEVLIRVEKNVGRITLNRPKALHALTLGMCETMIGALLDWQDDPEVYMVLIDHTGER 61 Query: 92 AFCAGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSV 151 FCAGGDI+ L+++ ++ F EY LN+ + + + P VA++DGI MGGGVG+S+ Sbjct: 62 GFCAGGDIRMLADSGAKDGVEARRFFHTEYQLNHLLFTYETPVVAVMDGIVMGGGVGISM 121 Query: 152 HGQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGI 211 R+ATER+ FAMPETGIGLFPDVGGG++LPRL GK G +LALTG R+KG D R GI Sbjct: 122 PAHIRIATERTTFAMPETGIGLFPDVGGGWYLPRLPGKAGLWLALTGARIKGADCMRLGI 181 Query: 212 ATHFVDSEKLHVLEEELLALKSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCF 271 ATHFV+ + L++ ++A + L Y A + G+ + FE+ ++++ F Sbjct: 182 ATHFVEFGAVEGLKKAIIA----DPRRIEETLRKYRADA--GKASLLGFEQDLNRL---F 232 Query: 272 SANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEGST-KTLQEVLTMEYR 330 +VE+I E L D S + Q++V+ SP +LK+ QL G+ + + + MEYR Sbjct: 233 VGESVEEIFEFLTLDSSDWGKAQLEVMKTKSPQTLKVAFEQLKRGAAMEDFADNMAMEYR 292 Query: 331 LTQACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSL 378 + + HDF EGVRAV++DKD P+W PA ++DVTD L F L Sbjct: 293 IGSRVVMKHDFIEGVRAVIVDKDNAPRWSPARVEDVTDAALAEIFAPL 340 Lambda K H 0.320 0.136 0.394 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: 304 Number of extensions: 14 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: 385 Length of database: 350 Length adjustment: 30 Effective length of query: 355 Effective length of database: 320 Effective search space: 113600 Effective search space used: 113600 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: 49 (23.5 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