Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate HSERO_RS22810 HSERO_RS22810 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__HerbieS:HSERO_RS22810 Length = 423 Score = 333 bits (855), Expect = 5e-96 Identities = 177/395 (44%), Positives = 233/395 (58%), Gaps = 13/395 (3%) Query: 49 LVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADF 108 LV+RG+Y+AR DC+ACHS AGK ++GGL + + G I++TNITPDK GIG YS A F Sbjct: 31 LVARGQYLARAGDCMACHSAAGKPAYSGGLAIDSGHGIIYSTNITPDKEHGIGNYSEAQF 90 Query: 109 DRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLN 168 AVRHGV G +LYPAMPYPSY K+SD+DI ALY +FMQG++P S + +P N Sbjct: 91 SAAVRHGVRADGTQLYPAMPYPSYAKVSDEDIHALYTYFMQGVQPVASTPPASSMSFPFN 150 Query: 169 MRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEA 228 +RW + LWN FA + + A RGAY+V+G GHCGSCHTPRG+A NEKA D + Sbjct: 151 IRWGMKLWNVFFANDKPFREQDGWSAEIKRGAYLVEGLGHCGSCHTPRGVAMNEKASDSS 210 Query: 229 GAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNST 288 A FL+G L+GW PSLR G+ WS IV +L+TGRN A V G M+ +ST Sbjct: 211 QAQFLSGGDLNGWAVPSLR-----GMPHWSAQDIVDYLQTGRNKTASVAGEMSLVVEHST 265 Query: 289 QFMQDDDLAAIARYLKSL-------PGDPQRDGAPWQYQAVAAVQDAP-GAHTYATRCAS 340 ++ +DL A+A YLK+L G G + A +D G Y CA+ Sbjct: 266 SHLKREDLQAMAAYLKTLSPVASSGSGRVIPQGVDATVSKLTAAKDLTLGERLYLDNCAA 325 Query: 341 CHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLS 400 CH + G+G P P L GAT A+ ++ +++ L G++ P MP F +LS Sbjct: 326 CHFVTGRGAPGIFPVLDGATVVNAENPSALLHVILAGARTPSTEKAPSILVMPGFAHRLS 385 Query: 401 DTEIAEVLSYVRSTWGNNGGAVDANAVGKLRGHTD 435 D E A + ++VR WGN+ G V VGKLR D Sbjct: 386 DEEAAALATFVRQGWGNHAGKVSEREVGKLRAGMD 420 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: 558 Number of extensions: 35 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: 447 Length of database: 423 Length adjustment: 32 Effective length of query: 415 Effective length of database: 391 Effective search space: 162265 Effective search space used: 162265 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