Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS05600 RR42_RS05600 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Cup4G11:RR42_RS05600 Length = 372 Score = 290 bits (743), Expect = 3e-83 Identities = 167/382 (43%), Positives = 228/382 (59%), Gaps = 15/382 (3%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 M+F+LS+EQ+ L ++V + YDF++RKK K + G S A WG E GL LP E Sbjct: 1 MNFNLSDEQKQLADAVHRFIDKDYDFETRKKGIKAEAGHSDAAWGALVELGLTALPVPEA 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 GGF ++ M+VM+ LG LV+EPY TVV L+ AG + A L + G Sbjct: 61 QGGFSGTPIDMMVVMQELGRGLVVEPYFATVVAAYA-LKLAGG---QDALLEQVAGGELK 116 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 A A E ++R+ L DV TAK G ++G K V ++G A L+V+ART G D + Sbjct: 117 LATAFNEPHARYALNDVRVTAK----GGKLNGRKVVTIHGAQAGKLVVSARTSGADADTS 172 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 G+ +FLV A G++ Y T D L AADITF Q +G A LIE V D A Sbjct: 173 GISLFLVDPKAAGVSITDYRTIDNLRAADITFKDAQ---GELLGTEGAAFALIEQVADYA 229 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 LCAEAVG++D T+EY KTR+QFGVPI FQ LQHR +MF+ EQ+RS+ + A Sbjct: 230 AVLLCAEAVGVIDTLNAATLEYAKTRQQFGVPIARFQALQHRMVEMFIHAEQSRSITLLA 289 Query: 301 TMAAEFDDA--KERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTM 358 AA+FD+A +ER +AAK ++G++ + VGQ+++Q+HGG+G+T E H FKRLT+ Sbjct: 290 --AAKFDEASPEERRRFASAAKARVGQAARSVGQEAVQIHGGMGVTDELPAAHMFKRLTL 347 Query: 359 IEQTFGDTDHHLARVSAGGGLI 380 I TFGD DHHL+R + G + Sbjct: 348 INTTFGDVDHHLSRFATQPGFL 369 Lambda K H 0.318 0.135 0.388 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: 375 Number of extensions: 17 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: 380 Length of database: 372 Length adjustment: 30 Effective length of query: 350 Effective length of database: 342 Effective search space: 119700 Effective search space used: 119700 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 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