Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Dyella79:N515DRAFT_0492 Length = 386 Score = 252 bits (643), Expect = 2e-71 Identities = 147/377 (38%), Positives = 214/377 (56%), Gaps = 6/377 (1%) Query: 38 TEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMD 97 TE+Q + + R+ A + I P A E+D FP+ LGL+ VP EYGG GMD Sbjct: 6 TEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYGGAGMD 65 Query: 98 ITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAFA 156 + + + EI A+T+ ++ + IL G+ K+KY+ + + A+A Sbjct: 66 PIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAI-GAYA 124 Query: 157 ATEPGAGSDLLAMKTRAVKKGD-KYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMST 215 TEP +GSD AM TRA K D +VING+K +IT+G VA + ++A + P GA+G+S Sbjct: 125 LTEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGARGVSA 184 Query: 216 FVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINR 275 F+++ PG G E K+G+R E+ F D P ENL+GEEGKGF+ MG L R Sbjct: 185 FIIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVLDAGR 244 Query: 276 VFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKAT 335 + ASQ+VGIA+ A E +Q +R+R+ FG+ I Q IADM +++AA LL +A Sbjct: 245 IGIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLTLRAA 304 Query: 336 TLLDAKDKRGPLIG---GMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLT 392 +K G G +AK AS+ AM + AVQ+ GG GY +E +ER R+AK+T Sbjct: 305 WTKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRDAKIT 364 Query: 393 QIYTGTNQITRMVTGRS 409 +IY GT++I R+V R+ Sbjct: 365 EIYEGTSEIQRLVIARA 381 Lambda K H 0.318 0.133 0.375 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: 366 Number of extensions: 11 Number of successful extensions: 4 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: 414 Length of database: 386 Length adjustment: 31 Effective length of query: 383 Effective length of database: 355 Effective search space: 135965 Effective search space used: 135965 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