Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate HSERO_RS06965 HSERO_RS06965 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__HerbieS:HSERO_RS06965 Length = 422 Score = 293 bits (749), Expect = 9e-84 Identities = 165/402 (41%), Positives = 223/402 (55%), Gaps = 16/402 (3%) Query: 38 QEQAGATFEP---ALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITP 94 +E+ AT P +++G+Y+AR +C+ACH+ G AP+AGG +A+P G ++ +NITP Sbjct: 24 EERGAATPAPDPTRQLAQGQYLARAGNCMACHTARGGAPYAGGRAIASPFGTLYTSNITP 83 Query: 95 DKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPA 154 DK+TGIG +S DF RA+ HG G+ LYPA PY SY +LS D AL+A ++Q + P Sbjct: 84 DKTTGIGQWSADDFWRALHHGRGKEGQFLYPAFPYTSYTRLSRADSDALFA-YLQSLPPV 142 Query: 155 NQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHT 214 + N + +P + R + LW ++ +Y P QDA WNRGAY+VQG GHC +CH+ Sbjct: 143 ARANQAHTLRFPYDQRMLLGLWRALYFTPQSYQPDPRQDAQWNRGAYLVQGAGHCSACHS 202 Query: 215 PR---GLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRN 271 R G + AL P L WYAP L + GL WS I LKTG + Sbjct: 203 ARNRLGASIEPLALAGGVIPALQ------WYAPPLHGGAD-GLQDWSTADIAALLKTGVS 255 Query: 272 AHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGA-PWQYQAVAAVQ-DAP 329 HAV G M+E S Q++ D D++A+A YLKSLP D A P + A + Sbjct: 256 PHAVTLGPMSEIVGRSLQYLNDADVSAMAVYLKSLPASAADDAARPASVEPAEAERIMKQ 315 Query: 330 GAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDA 389 G Y T C CHG G+G PPLAG + A+A+ LNG +G P Sbjct: 316 GKQLYGTLCVDCHGGKGQGSAPDYPPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGNPYP 375 Query: 390 YRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLR 431 + MP F QLSD E+A V+SYVR++WGN GG V A V + R Sbjct: 376 FGMPPFGPQLSDQEVAAVVSYVRNSWGNQGGLVSAAEVNRYR 417 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: 673 Number of extensions: 46 Number of successful extensions: 6 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: 422 Length adjustment: 32 Effective length of query: 415 Effective length of database: 390 Effective search space: 161850 Effective search space used: 161850 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