Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_009778630.1 MED217_RS01145 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_000152985.1:WP_009778630.1 Length = 392 Score = 211 bits (538), Expect = 2e-59 Identities = 120/373 (32%), Positives = 203/373 (54%), Gaps = 5/373 (1%) Query: 6 LSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSYI 65 L+E+ +++R ARD+ +R+++P + + ++ + E+G G +PEE+GG+ + Sbjct: 18 LTEEHKLVRSAARDWVKRDVSPIIEEAAQKAEFPKEIIKGLAEIGAFGPYIPEEYGGAGL 77 Query: 66 DYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCFA 125 D ++Y L ++EI GD + S+ +S+ P+ +G++ Q+ ++L +LASG +GCF Sbjct: 78 DQISYGLIMQEIERGDSGVRSTASVQSSLVMYPIFKFGTEVQRKKYLPKLASGEFMGCFG 137 Query: 126 LTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSAF 185 LTEP GS + T + H++LNG+K + SNA + +A+V+A E G+ + Sbjct: 138 LTEPDHGSNPGGMVTNFKDKGDHYLLNGAKMWISNAPFADIAVVWA--KDESGR--IHGL 193 Query: 186 LVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGRI 245 +V GF+ + +K +RAS T + + +IP+ NLL + GL L L+ R Sbjct: 194 IVERGMEGFSTPTTHNKWSLRASATGELIFDNVKIPKENLLPNK-SGLGAPLMCLDSARF 252 Query: 246 GIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAAR 305 GI A+G A ++ AL YA+ER QFGKPI Q LA+M T++ A+LL Sbjct: 253 GIAWGAIGAAMDCYDTALRYAKEREQFGKPIGSFQLQQKKLAEMITEITKAQLLAWRLGA 312 Query: 306 LKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEG 365 L++ ++ S AK EMA K+ +A QI GG G +Y + R+ + YEG Sbjct: 313 LRNEDKATSAQISMAKRNNVEMALKIAREARQILGGMGITGEYSIMRHMMNLESVVTYEG 372 Query: 366 SSEIQRLLIAREL 378 + +I L+ ++ Sbjct: 373 THDIHLLITGMDI 385 Lambda K H 0.318 0.133 0.390 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: 327 Number of extensions: 11 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: 383 Length of database: 392 Length adjustment: 30 Effective length of query: 353 Effective length of database: 362 Effective search space: 127786 Effective search space used: 127786 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