Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate PP_3948 PP_3948 nicotinate dehydrogenase subunit B
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Putida:PP_3948 Length = 1187 Score = 247 bits (631), Expect = 1e-69 Identities = 154/417 (36%), Positives = 213/417 (51%), Gaps = 32/417 (7%) Query: 6 FARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVAC 65 F AG + A L W P TP ++ A++ RG VA DC C Sbjct: 766 FGSLAGVFGAALGMLATALPWRAEIAPVTP----PGVGSWSAAMLERGRQVAAAGDCAVC 821 Query: 66 HSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYP 125 H+++G AGGL M TP G +++TNITPD TGIG +S A F+RA+R G++ GR LYP Sbjct: 822 HTVSGGKANAGGLAMDTPFGTLYSTNITPDPETGIGRWSFAAFERAMREGISRDGRHLYP 881 Query: 126 AMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTAT 185 A PY S+ ++D D++ALYA+ M P Q + + +P N R +A WN F Sbjct: 882 AFPYTSFRNINDADMQALYAYLMSQ-TPVRQEAPANQMRFPFNQRPLMAGWNARFLQRGE 940 Query: 186 YAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPS 245 Y P + A WNRGAY+V G GHC +CH+PR L EK G+ +LAG ++DGW AP+ Sbjct: 941 YQPDPQRSAQWNRGAYLVDGLGHCTACHSPRNLMGAEK----GGSSYLAGGMVDGWEAPA 996 Query: 246 LRQDPNTGLGR----WSEPQIVQFLKTG-RNAHAVVYGSMTEAFNNSTQFMQDDDLAAIA 300 L LG+ WSE ++ +L TG H V G M + + D+ AIA Sbjct: 997 L-----NALGKSSTPWSEDELFNYLSTGFSEKHGVAAGPMGPVVSELAT-LPKSDVRAIA 1050 Query: 301 RYLKSLPGDPQRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGLDGKGQPEWMPPLAGAT 360 YL SL G+PQ A Q V + G + C CH DG G P L G + Sbjct: 1051 HYLSSLEGEPQALAANAAPQVDTHVSLSNGERVFKGACLGCHS-DGLG-----PKLFGVS 1104 Query: 361 SALAKESASAINITLNGSQRVVASGVP-----DAYRMPAFREQLSDTEIAEVLSYVR 412 ++A S ++ N RVV G+P D MP F++ LSD ++A++ +Y+R Sbjct: 1105 PSMAVNSNVHSDLPDN-LLRVVLHGIPTPATRDLGYMPGFKDSLSDRQVADLAAYLR 1160 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: 1500 Number of extensions: 78 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: 1187 Length adjustment: 40 Effective length of query: 407 Effective length of database: 1147 Effective search space: 466829 Effective search space used: 466829 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: 55 (25.8 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