Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_084199172.1 C0029_RS09065 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF1051 (387 letters) >NCBI__GCF_002869505.1:WP_084199172.1 Length = 378 Score = 270 bits (689), Expect = 7e-77 Identities = 146/372 (39%), Positives = 212/372 (56%), Gaps = 1/372 (0%) Query: 12 ETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGY 71 E + + R+ + EI P E ++++L P ++W G GLL + E YGGAG Sbjct: 4 EELTLFRDMARRAYEQEIEPHYEGWEEQHLVPRELWNTLGAAGLLCPDMPEAYGGAGTSP 63 Query: 72 LAHVVAMEEISR-GSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAM 130 + +EE+SR G +A YG HSN+ IN G EQK ++LPK+I+GE VGALAM Sbjct: 64 RVCLAMIEEMSRMGFGGLASGYGIHSNIVAPYINHFGTEEQKQQWLPKMITGEAVGALAM 123 Query: 131 SEPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFI 190 +EP AGSDV ++ A + G+ +VLNGSK +ITNG A+ ++ A TD KGA G + F+ Sbjct: 124 TEPGAGSDVQGIRTTAVRDGEEWVLNGSKIFITNGIHADLVIVAAITDPGKGAKGTSLFL 183 Query: 191 VERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLDYERVV 250 V+ GF +GNK +K+G S+T ELFF DV +P +LG EN G ++M+ L ER+ Sbjct: 184 VDASLPGFEKGNKIEKIGQHASDTAELFFQDVRLPASALLGEENKGFVIMMTELPRERLG 243 Query: 251 LAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQA 310 +A + +D+ V Y+ +RK FGQ++ FQ + +A++ T++ +RA A Sbjct: 244 IAAQAVAAAEGAMDITVDYVLERKAFGQTVASFQNTRFTLAEVKTEIALNRALYEKCADD 303 Query: 311 CDRGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYEIGAGT 370 RGE T DAA + E Q +Q+ GG GY E+P R DA++ I GT Sbjct: 304 YARGELTADDAAMLKYANTEMQCSTIDQCLQLFGGYGYTAEYPISRYYTDARIQRIYGGT 363 Query: 371 SEIRRMLIGREL 382 SEI R L+ R + Sbjct: 364 SEIMRELVARSI 375 Lambda K H 0.318 0.135 0.391 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: 396 Number of extensions: 21 Number of successful extensions: 2 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: 387 Length of database: 378 Length adjustment: 30 Effective length of query: 357 Effective length of database: 348 Effective search space: 124236 Effective search space used: 124236 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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