Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_01369 CCNA_01369 acyl-CoA dehydrogenase, short-chain specific
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Caulo:CCNA_01369 Length = 379 Score = 358 bits (918), Expect = e-103 Identities = 188/373 (50%), Positives = 248/373 (66%), Gaps = 5/373 (1%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQ-GLLGLPFSE 59 MDF+ +EEQ ++++SV L+ YDFD+R+K GW W FAE+ G+LG FSE Sbjct: 1 MDFNFTEEQSMVRDSVASFLQDKYDFDTRRKIVSSDAGWRADYWKAFAEELGILGASFSE 60 Query: 60 EDGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSK 119 E GG G GA++ MI+ME G +LV+EPYL TVVIGGGF++ +G A A+ + GI+ GS Sbjct: 61 ELGGLGGGAIDNMIIMEEFGKALVIEPYLGTVVIGGGFMKHSGYAGA-ASVIEGIVGGST 119 Query: 120 TFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDR 179 T AFA E +R+ D+ TTAKK G GWV++G K VV+ A LIVTART G QRD Sbjct: 120 TIAFAYAEPQARYTWQDLKTTAKKDGSGWVLNGHKAVVVGAPFATHLIVTARTGGAQRDA 179 Query: 180 TGVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDD 239 GVGVF++ G+ + YPT DG A+++ F V + A+A I E+ L L+E V+D+ Sbjct: 180 GGVGVFIIDKSLPGVVTRDYPTVDGNRASEVYFENVSIPAEALIS--ESGLALVEQVMDE 237 Query: 240 ARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMF 299 A A+ AEAVG++ + T++Y K RKQFG I +FQVLQHR DMF+ EQ+ SM Sbjct: 238 AIAAVGAEAVGVLRKLHEGTLDYAKQRKQFGTAIANFQVLQHRMVDMFIEVEQSVSMTYM 297 Query: 300 ATMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMI 359 AT+ + A ERA A++A KV+IG++ KFVGQ +IQ+HGG+GMT E IGHYFKR TMI Sbjct: 298 ATIKVG-ESAAERAKAVSAMKVRIGRACKFVGQSAIQIHGGMGMTDELAIGHYFKRATMI 356 Query: 360 EQTFGDTDHHLAR 372 E FG DHHL R Sbjct: 357 EGLFGSVDHHLKR 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: 442 Number of extensions: 20 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: 380 Length of database: 379 Length adjustment: 30 Effective length of query: 350 Effective length of database: 349 Effective search space: 122150 Effective search space used: 122150 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