Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate AO353_10800 AO353_10800 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10800 Length = 435 Score = 399 bits (1025), Expect = e-115 Identities = 204/402 (50%), Positives = 258/402 (64%), Gaps = 11/402 (2%) Query: 48 ALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLAD 107 AL+ +GEY+AR DCVACH+ G PFAGGL M TP+G I++TNITPDK TG+G YS D Sbjct: 26 ALIKQGEYLARAGDCVACHTAKGGKPFAGGLPMETPIGTIYSTNITPDK-TGLGDYSFDD 84 Query: 108 FDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPL 167 FD+AVRHGVA G LYPAMPYPSY ++SD D+KALYA+FM+G+ P Q N SDIPWPL Sbjct: 85 FDKAVRHGVAKNGSTLYPAMPYPSYARVSDADMKALYAYFMKGVAPVTQENKGSDIPWPL 144 Query: 168 NMRWPIALWNGVFAPT-ATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALD 226 +MRWP+ W +FAP+ Y ++A +RGAY+V+G GHCG+CHTPR L EKAL Sbjct: 145 SMRWPLTGWRWMFAPSVVAYQPADGKEAAISRGAYLVEGLGHCGACHTPRALTMQEKALS 204 Query: 227 -EAGAPFLAG-ALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAF 284 G+ FL+G A L+GW A SLR D GLG WSE Q+VQFLKTGR+ + V+G M++ Sbjct: 205 ANEGSAFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSAVFGGMSDVV 264 Query: 285 NNSTQFMQDDDLAAIARYLKSLP-GDPQRDGAPWQYQAVAAV----QDAPGAHTYATRCA 339 +S Q+M DDDL AIARYLKSLP DP P+ Q A+ PGA Y CA Sbjct: 265 EHSMQYMSDDDLTAIARYLKSLPANDPNDQPHPYDPQVAQALWKGDDSKPGASVYIDNCA 324 Query: 340 SCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQL 399 +CH DG G P LAG + + S INI L G+ P + MPAF +L Sbjct: 325 ACHRTDGHGYTRVFPALAGNPVLQSDDPVSLINIVLKGATLPATHTAPSTFTMPAFAWRL 384 Query: 400 SDTEIAEVLSYVRSTWGNNGGAVDANAVGKLRGHTDPASSSP 441 SD E+A+V++++R++WGN G + V +R D S P Sbjct: 385 SDQEVADVVNFIRTSWGNKGAQIKPADVADVR--KDEVKSMP 424 Lambda K H 0.318 0.133 0.423 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: 664 Number of extensions: 44 Number of successful extensions: 7 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: 447 Length of database: 435 Length adjustment: 32 Effective length of query: 415 Effective length of database: 403 Effective search space: 167245 Effective search space used: 167245 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: 51 (24.3 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