Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_012333698.1 M446_RS18850 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_000019365.1:WP_012333698.1 Length = 376 Score = 256 bits (655), Expect = 6e-73 Identities = 152/376 (40%), Positives = 220/376 (58%), Gaps = 5/376 (1%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 L+++Q L D R A + P A E D S FP A +LG L L+P AYGG+ + Sbjct: 2 LSDDQILIRDTARSFAQARLRPFAAEWDRDSRFPREAVAALGELGFLGMLVPEAYGGSAV 61 Query: 64 GVLTLALILEEL--GRVCASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTA 121 ++ AL +EE+ G ST ++ + + +PI+ G+ KER+L A L A Sbjct: 62 DHVSYALAIEEIAAGDGAVST-IMSVHNSVACVPILRFGTEAQKERFLVPLA-RGAQLGA 119 Query: 122 LAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGIS 181 TEP AGSD A+ RA R G++YV++G K FIT+G AD+ +V+A TDPE G +GIS Sbjct: 120 FCLTEPGAGSDAGAVTARARRVGNRYVLSGTKQFITSGRSADLAIVFAVTDPEAGKRGIS 179 Query: 182 AFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTN 241 AF+V TPG R E K+G R S +++ FE+ME+ + ++G EG G + L Sbjct: 180 AFIVPTATPGYRVARIEHKLGQRASDTAQIVFEDMELTPDLLLGQEGEGLRIALSNLEGG 239 Query: 242 RVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKA 301 R+ AAQAVG+A+ A + A+ + +R FG+ + V F +ADMAT +EA+RLL A Sbjct: 240 RIGIAAQAVGMARAAFEAALAYAGERETFGQKLTAHQAVAFRLADMATRIEAARLLVHNA 299 Query: 302 AELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQI 361 A L D G + + +MAK AS+ A V +DA+Q+ GG GY+ + VER+ RD ++ QI Sbjct: 300 ARLRDAG-QPCLKEAAMAKLFASEMAEAVCSDAIQIHGGYGYLADYPVERIYRDVRVCQI 358 Query: 362 YTGTNQITRMVTGRAL 377 Y GT+ + R+V RAL Sbjct: 359 YEGTSDVQRIVISRAL 374 Lambda K H 0.319 0.134 0.371 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: 307 Number of extensions: 18 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: 376 Length adjustment: 30 Effective length of query: 350 Effective length of database: 346 Effective search space: 121100 Effective search space used: 121100 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 (21.7 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