Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_111395068.1 CLV31_RS21080 acyl-CoA dehydrogenase
Query= BRENDA::Q60759 (438 letters) >NCBI__GCF_003253485.1:WP_111395068.1 Length = 452 Score = 228 bits (581), Expect = 3e-64 Identities = 132/350 (37%), Positives = 195/350 (55%), Gaps = 5/350 (1%) Query: 87 NRNEVFHRDIVYEMGELGVLGPTIKGYGCAGVSSVAYGLLTRELERVDSGYRSMMSVQSS 146 NR E F I+ +M EL + G T +GYGC G S++ G + E+ RVD+ + VQS Sbjct: 105 NRAE-FPMHIIPKMAELNIAGLTYQGYGCPGHSALLEGFIAMEMARVDTSISTFFGVQSG 163 Query: 147 LVMHPIYTYGSEEQRQKYLPGLAKGELLGCFGLTEPNHGSDP-GGMETRARHNPSNQSYT 205 L M +Y GSE Q+Q++LP + K E +G FGLTEP GS GG+ T + + Sbjct: 164 LAMGSVYLCGSEAQKQEWLPAMQKLEKIGAFGLTEPEVGSGAAGGLTTTCKRE--GDVWI 221 Query: 206 LSGTKTWITNSPVADLFIVWAR-CEDNCIRGFILEKGMRGLSAPRIEGKFSLRASATGMI 264 L+G K WI N+ +D+ ++WAR +DN ++GFI+ KG G A +++ K +LR +I Sbjct: 222 LNGQKKWIGNATFSDMTVIWARDLDDNQVKGFIVRKGNPGFQAEKLKDKMALRTVQNALI 281 Query: 265 IMDSVEVPEENVLPNVSSLAGPFGCLNTARYGITWGVLGAAEFCLHTARQYALDRIQFGV 324 + + EVPE + L + +S L R G+ W +G A A Y +R QFG Sbjct: 282 TLTNCEVPESDRLQSANSFKDTAKVLRMTRAGVAWQAVGCARGAYELALAYTNERQQFGR 341 Query: 325 PLARNQLVQKKLADMLTEITLGLHACLQLGRLKDQDKATPEMVSMLKRNNCGKALDIARQ 384 P+A QLVQ L ML ++T +L +++DQ + E S+ K + I Sbjct: 342 PIASFQLVQDLLVTMLGDLTAMQTMVFRLSQMQDQGELLDEHASLAKVFCTLRMRSIVDH 401 Query: 385 ARDILGGNGISDEYHVIRHAMNLEAVNTYEGTHDIHALILGRAITGIQAF 434 AR++ GGNGI ++ + R + EAV +YEGT +I++LI+GRAITG AF Sbjct: 402 ARELFGGNGILLQHDIARFVADAEAVYSYEGTKEINSLIVGRAITGHSAF 451 Lambda K H 0.320 0.136 0.408 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: 373 Number of extensions: 10 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: 438 Length of database: 452 Length adjustment: 32 Effective length of query: 406 Effective length of database: 420 Effective search space: 170520 Effective search space used: 170520 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: 51 (24.3 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