Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate PP_2479 PP_2479 Cytochrome c family protein
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Putida:PP_2479 Length = 407 Score = 248 bits (633), Expect = 3e-70 Identities = 141/387 (36%), Positives = 206/387 (53%), Gaps = 15/387 (3%) Query: 49 LVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADF 108 L+++GEY+ R ++CVACH++ G PFAGG+E P G++ + NITPD TGIG ++ +F Sbjct: 27 LLAKGEYLTRAANCVACHTVPGGQPFAGGVEFKLPFGSLFSPNITPDPQTGIGAWTDDEF 86 Query: 109 DRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLN 168 A++ G+ G+ YPA PY SY K+S DDI A+ ++ ++P Q + I +P N Sbjct: 87 VSALQTGIGRDGKHYYPAFPYTSYSKMSRDDILAIKG-YLDSLQPVEQAPRENHIGFPFN 145 Query: 169 MRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEA 228 RW + WN +F + A + A WNRG Y+V+GPGHCG CH+PR L F + + + Sbjct: 146 QRWGMVFWNLLFLNDEPFQADSQRSAEWNRGKYLVEGPGHCGECHSPRNL-FQAVSSERS 204 Query: 229 GAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTG-RNAHAVVYGSMTEAFNNS 287 LAG L+ GW A ++ DP G+G W + +LK G + G M E NS Sbjct: 205 ----LAGNLIQGWNAYNISADPVHGIGAWPTDVLAGYLKDGAAPGLGLSSGPMAEVVENS 260 Query: 288 TQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAAVQ---DAPGAHTYATRCASCHGL 344 + + D D AIA +LK P P+ +G P Q A A G +A CASCH Sbjct: 261 LRHLTDADRQAIAVFLKDSP--PRSEGVPRPQQVTLAEPGSGSALGNKLFAEACASCHRW 318 Query: 345 DGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEI 404 DG G L G + +++ + I L+G A+ P RMP+F +D E+ Sbjct: 319 DGTGNQSQTAMLLGLKTVNDPAASNLLGILLSGHG---AADAPVNRRMPSFGNIYTDQEL 375 Query: 405 AEVLSYVRSTWGNNGGAVDANAVGKLR 431 A + S++ +G +G V AV K R Sbjct: 376 AALSSFMLQRFGESGAQVSVPAVAKRR 402 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: 557 Number of extensions: 25 Number of successful extensions: 8 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: 407 Length adjustment: 32 Effective length of query: 415 Effective length of database: 375 Effective search space: 155625 Effective search space used: 155625 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