Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate Ac3H11_1933 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)
Query= SwissProt::Q9FS87 (412 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1933 Length = 386 Score = 253 bits (647), Expect = 5e-72 Identities = 145/379 (38%), Positives = 214/379 (56%), Gaps = 8/379 (2%) Query: 33 LFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPEEYGG 92 LF + F +S +F ++ + PH + Y ++V W G L +++PEEYGG Sbjct: 6 LFQPEHQAFADSFRRFIEKEVTPHHADWEDQGYVAREV--WSQAGANGFLCMSLPEEYGG 63 Query: 93 LGLGYLYHCIAMEEISRASGSVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLISGEHVG 152 G LY MEE++RA G+ G+ +G H+ + ++ GT EQK+KYLP++ SG VG Sbjct: 64 AGADKLYSVAQMEELARA-GTTGIGFGLHSEIVAPYILHYGTEEQKRKYLPQMASGAVVG 122 Query: 153 ALAMSEPNAGSDVVSMKCKADRVEGG--YVLNGNKMWCTNGPTAQTLVVYAKTDVTAGSK 210 A+AMSEP AGSD+ +K A + G YVLNG+K + TNG A ++V AKTD AG+K Sbjct: 123 AIAMSEPAAGSDLQGIKTTAIKSADGSHYVLNGSKTFITNGWHADLVIVVAKTDPAAGAK 182 Query: 211 GITAFIIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLG---QVGRGVYVLM 267 G + ++E+GM GF Q+L KLGM+ DT EL F + VP EN+LG GRG LM Sbjct: 183 GTSLLLVERGMPGFEKGQRLKKLGMKAQDTSELFFNDVKVPAENLLGGPAMEGRGFICLM 242 Query: 268 SGLDLERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSR 327 L ERL +A V QA +D L YVK+R+ FG+P+ FQ + +A++ T +Q +R Sbjct: 243 EQLPWERLQIAITAVAAAQAAIDWTLDYVKERKVFGQPVASFQNTRYTLAELQTEVQVAR 302 Query: 328 SYLYSVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDA 387 ++ ++T+ + + +V + +Q GG GY+ EYP R DA Sbjct: 303 VFVDKCCELIARDQLDTQTASMAKYWTTDLQCKVMDECVQMFGGYGYMWEYPITRAYADA 362 Query: 388 KLYEIGAGTSEIRRMIIGR 406 ++ I GT+EI + +I R Sbjct: 363 RVQRIYGGTNEIMKEVISR 381 Lambda K H 0.319 0.135 0.396 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: 382 Number of extensions: 21 Number of successful extensions: 5 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: 412 Length of database: 386 Length adjustment: 31 Effective length of query: 381 Effective length of database: 355 Effective search space: 135255 Effective search space used: 135255 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 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