Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_078210577.1 BXU11_RS00155 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_002017945.1:WP_078210577.1 Length = 392 Score = 399 bits (1024), Expect = e-115 Identities = 200/386 (51%), Positives = 266/386 (68%) Query: 8 FDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLG 67 F D LD LT+ ++VRD+ARA+ + + P +++ + + + I +GE+G G Sbjct: 6 FQSPDYYNLDDLLTEEHKLVRDAARAWVKREVSPIIEDYAQKAEFPKQIIKGLGEIGGFG 65 Query: 68 ATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLP 127 IP +YGG+G++ + YGLI +E+ER DSG RS SVQSSLVM PI ++G+EE + KYLP Sbjct: 66 PYIPVEYGGAGLDQISYGLIMQEIERGDSGVRSTSSVQSSLVMYPIWKYGNEEQRMKYLP 125 Query: 128 KLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKD 187 KLATGE++GCFGLTEP+HGS+PG M T + Y L+GAKMWI+N+P AD+ VVWAK+ Sbjct: 126 KLATGEFMGCFGLTEPDHGSNPGGMTTNFKDKGDHYLLNGAKMWISNAPFADIAVVWAKN 185 Query: 188 DAGDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFT 247 + G I G ++E+G +G + P H K LRAS TGE++ D V P+EN P GL P Sbjct: 186 EEGRIHGLIVERGMEGFTTPETHNKWSLRASATGELIFDNVKVPKENLLPNKSGLGAPLG 245 Query: 248 CLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQ 307 CL+SARYGIAWGA+GAA CY+TA +Y +R QF +P+A QL QKKLA+M+TEIT Sbjct: 246 CLDSARYGIAWGAIGAAMDCYDTALRYAKERIQFDKPIAGTQLQQKKLAEMITEITKAQL 305 Query: 308 GCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLE 367 RLG L++EG A S+ KRN+ ++ IAR AR MLGG GI+ E+ I RH++NLE Sbjct: 306 LTWRLGVLRNEGRATSAQISMAKRNNVDMAIHIAREARQMLGGMGITGEYSIMRHMMNLE 365 Query: 368 VVNTYEGTHDIHALILGRAITGLAAF 393 V TYEGTHDIH LI G ITG++AF Sbjct: 366 SVITYEGTHDIHLLITGMDITGISAF 391 Lambda K H 0.319 0.136 0.409 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: 431 Number of extensions: 8 Number of successful extensions: 1 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: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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: 50 (23.9 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