Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 7024806 Shewana3_1984 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= BRENDA::P26440 (426 letters) >FitnessBrowser__ANA3:7024806 Length = 585 Score = 120 bits (301), Expect = 1e-31 Identities = 111/378 (29%), Positives = 174/378 (46%), Gaps = 44/378 (11%) Query: 84 WKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGL--SYGAHSNLCINQLV 141 + Q G +G+ ++GG G+ + VLV E A A L S A + LCIN Sbjct: 84 YDQYSQGGWVGLCGEPEFGGMGMPKMLGVLVDEMAYSACNAFTLYGSLTAGAALCINA-- 141 Query: 142 RNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKA-EKKGNHYILNGNKFWIT 200 +G+E KE YLPKL SGE+ GA+ M+EP AGSD+ +++ +A + Y ++G+K +IT Sbjct: 142 -HGSEEIKETYLPKLYSGEWAGAMDMTEPQAGSDLRNIRTRAIPQDDGSYAISGSKIFIT 200 Query: 201 NGPDADVLIVYAKTDLAAVPASRGITAFIVEK----------GMPGFSTSKKLDKLGMRG 250 G D D+ LA +P S+GI+ F+V K G S K+G++G Sbjct: 201 GG-DHDLTENVIHLVLAKLPESKGISLFLVPKTTVNADGSLGQANGVSVGSIEHKMGLKG 259 Query: 251 SNTCELIFEDCKIPAANILGHENKGVYVLMSGLDLERLVLAGGPLGLMQAVLDHTIPYLH 310 S TC + F++ K ++G N+G+ + + ++ ERL + LG QA Y Sbjct: 260 SATCVMNFDEAK---GYLIGEPNRGLVCMFTMMNYERLAIGIQGLGSAQAAYQMAADYAK 316 Query: 311 VRE----AFGQKIGHFQ---LMQGKMADMYTRLMAC----RQYVYNVAKACD-----EGH 354 R A G G ++ G + M + A R K D EG Sbjct: 317 ERNQGVAAGGSPTGSDSDPIIVHGDVRRMLLTIRAMTEAGRALSVFTGKQLDLAKYAEGE 376 Query: 355 CTAKDCAGVILYSAECATQVALDGI-------QCFGGNGYINDFPMGRFLRDAKLYEIGA 407 AK V L + + G+ Q FGG+GYI + + + +RD ++ +I Sbjct: 377 VKAKAARYVGLLTPVAKAFLTDRGLDATIMAQQVFGGHGYIRETGIEQLVRDTRIAQIYE 436 Query: 408 GTSEVRRL-VIGRAFNAD 424 GT+ ++ + +GR D Sbjct: 437 GTNGIQAIDFLGRKVTGD 454 Lambda K H 0.321 0.137 0.410 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: 521 Number of extensions: 33 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 426 Length of database: 585 Length adjustment: 34 Effective length of query: 392 Effective length of database: 551 Effective search space: 215992 Effective search space used: 215992 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: 52 (24.6 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