Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate RR42_RS21615 RR42_RS21615 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Cup4G11:RR42_RS21615 Length = 1000 Score = 235 bits (600), Expect = 4e-66 Identities = 150/431 (34%), Positives = 210/431 (48%), Gaps = 22/431 (5%) Query: 4 RRFARTAGWLALPCLVAAGLLAWYVT-REPATPFEQEQAGATFEPALVSRGEYVARLSDC 62 R AR WL AAGL + R P P AG + A + RG VA DC Sbjct: 558 RGAARKRNWLLAGATAAAGLFVTAMPWRAPIAPVAPPGAGF-YSAATIERGRLVAAAGDC 616 Query: 63 VACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRR 122 CH+ A AGGL + TP G I++TNITPD TGIG +S A F+RA+R G+ GR Sbjct: 617 AVCHTAPNGARNAGGLALDTPFGTIYSTNITPDVETGIGNWSYAAFERAMRQGIHRDGRH 676 Query: 123 LYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAP 182 LYPA PY ++ K SD D++ALYA+ M +P + + +P N+R +A WN +F Sbjct: 677 LYPAFPYTAFAKTSDGDLQALYAYLM-AAEPVRAKAPETALAFPYNLRPLMAGWNLLFHS 735 Query: 183 TATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWY 242 + A P + A WNRGAY+ +G GHC +CH+PR N ++ G +L G +GW Sbjct: 736 PKPFEADPARSAQWNRGAYLAEGLGHCSACHSPR----NALGAEQGGRRYLGGGEAEGWE 791 Query: 243 APSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARY 302 AP+L + + + W+E + +L+TG H + ++D+ AIA Y Sbjct: 792 APALGKLSHAPV-PWTEQALFSYLRTGYAPHHGAAAGPMAPVIEELALLPEEDVRAIAHY 850 Query: 303 LKSLPGDPQRDGAPWQYQA---------VAAVQDAPGAHTYATRCASCHGLD-GKGQPEW 352 + S GD Q D A QA A P A Y CA CH D G Q Sbjct: 851 VASF-GDAQPDAALASAQARQLEQRSADAARTLGGPAARLYQNACAVCHQSDQGIRQFGI 909 Query: 353 MPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVR 412 P LA T+ + + I + L+G + G D MPAF E L D ++ +++ Y+R Sbjct: 910 KPSLALNTNLHGDKPDNLIRVLLDG---IPTPGTSDLGYMPAFGESLDDRQLTQLVHYLR 966 Query: 413 STWGNNGGAVD 423 + + A D Sbjct: 967 KRFAPDKPAWD 977 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: 1376 Number of extensions: 77 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: 1000 Length adjustment: 38 Effective length of query: 409 Effective length of database: 962 Effective search space: 393458 Effective search space used: 393458 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: 54 (25.4 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