Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate H281DRAFT_03306 H281DRAFT_03306 Cytochrome c, mono- and diheme variants
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Burk376:H281DRAFT_03306 Length = 434 Score = 376 bits (965), Expect = e-109 Identities = 185/414 (44%), Positives = 252/414 (60%), Gaps = 18/414 (4%) Query: 28 VTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAI 87 VT EPA + A ALV+RGEY+A+ SDC CH+ G + GGL + +P G I Sbjct: 24 VTAEPAGASDPALA------ALVARGEYLAKASDCAGCHTAVGGQAYGGGLGLTSPFGTI 77 Query: 88 HATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFF 147 ++NITPD+ GIG YS DF R+VR GV+PG +RLYPAMPY S+ K+SDDD++ALYA+F Sbjct: 78 MSSNITPDRRYGIGAYSYEDFARSVREGVSPGNKRLYPAMPYASFSKMSDDDMRALYAYF 137 Query: 148 MQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPG 207 M G+KPA +P P+ + +P N RW + W FAPT Y K +DA WNRGA++VQGPG Sbjct: 138 MHGVKPAPEPAPPTKLAFPFNQRWVLYFWQLAFAPTEPYRPKAGRDAQWNRGAFLVQGPG 197 Query: 208 HCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLK 267 HCG+CHTPRG F E+ DE+ +L G + D W+ P+L DP +GLGR E + FLK Sbjct: 198 HCGACHTPRGPGFQERGYDESSPMYLTGGVNDNWFGPNLTGDPGSGLGRIGEKDLAAFLK 257 Query: 268 TGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAAVQ- 326 TG A V +GSM E +STQ++ D+D A+A Y+KSLP Q+ ++ A + Sbjct: 258 TGHGAGLVAFGSMVEQVEDSTQYLTDEDALAMAHYVKSLPA--QKPSGSYEPHAQPDLPT 315 Query: 327 ------DAP---GAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNG 377 DAP GA Y + CA CHG+ G G P P LAG S + +++ S I + + G Sbjct: 316 RNGNRVDAPQSVGARVYISFCARCHGVQGAGMPNVFPRLAGNPSVITEDTTSLIRLMVEG 375 Query: 378 SQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLR 431 P MP F + L++ ++A VLS++R++WGN+ V AN + LR Sbjct: 376 GNSPATISGPPRQAMPGFAQTLTNAQMANVLSWIRTSWGNDARPVTANDIQSLR 429 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: 666 Number of extensions: 45 Number of successful extensions: 2 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: 434 Length adjustment: 32 Effective length of query: 415 Effective length of database: 402 Effective search space: 166830 Effective search space used: 166830 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