Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate Echvi_1808 Echvi_1808 Cytochrome c.
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Cola:Echvi_1808 Length = 330 Score = 87.8 bits (216), Expect = 4e-22 Identities = 89/294 (30%), Positives = 134/294 (45%), Gaps = 55/294 (18%) Query: 28 VQQGEYLAR-AGDCVACHTAKDGKPFAG------------------GLPMETPIGVIYST 68 + +GEYLA C+ CH+ ++ F+G GLP GV S Sbjct: 48 IARGEYLANHVMLCMDCHSDRNYSLFSGPPHPGTKGLGGDRFDRSMGLP-----GVFVSP 102 Query: 69 NITPDKTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGV 128 NITP+ GIG+++ + + + GV K G ++P MP+ SY ++ D++A+ AY ++ + Sbjct: 103 NITPE--GIGNWTDGELYRLITTGVKKNGEPIFPVMPYQSYGKLDPEDIKAVIAY-IRTL 159 Query: 129 APVARDNQDSDIPWPLSMRWPLS-IWRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHC 187 AP Q S+IP P + +P++ I R M PS TP + VI+ G YLV C Sbjct: 160 AP-----QKSNIP-PREIDFPVNFIIRTM--PSKATPTTRPNKEDVIAYGEYLVTAAA-C 210 Query: 188 GACHTPRALTMQEKALSASGGSDFLSGS----APLEGWIAKSLRGDHKDGLGSWSEEQLV 243 G CHT K +L G +P + S H GLG+ S+E V Sbjct: 211 GECHT--------KFEKGKFVGPYLGGGRAFPSPNGNIVRSSNLTFHSTGLGNKSKEDFV 262 Query: 244 QFLKTGRSD---RSAVFGGMSDVVVHSMQY--MTDADLTAIARYLKSL-PANDP 291 + K + + V G ++ Y M DL +I YL+SL P N+P Sbjct: 263 RQFKQYSPELYTPTKVGEGEFQTIMPWTMYAGMDTTDLASIYEYLRSLEPINNP 316 Score = 52.0 bits (123), Expect = 3e-11 Identities = 35/131 (26%), Positives = 59/131 (45%), Gaps = 14/131 (10%) Query: 14 SAAANAAEADQQALVQQGEYLARAGDCVACHTAKD-----GKPFAGGLPMETPIG-VIYS 67 S A +++ ++ GEYL A C CHT + G GG +P G ++ S Sbjct: 184 SKATPTTRPNKEDVIAYGEYLVTAAACGECHTKFEKGKFVGPYLGGGRAFPSPNGNIVRS 243 Query: 68 TNITPDKTGIGDYSFEDFDKAVRH-------GVAKGGSTLYPAMPFPSYARVSDADMQAL 120 +N+T TG+G+ S EDF + + G MP+ YA + D+ ++ Sbjct: 244 SNLTFHSTGLGNKSKEDFVRQFKQYSPELYTPTKVGEGEFQTIMPWTMYAGMDTTDLASI 303 Query: 121 YAYFMKGVAPV 131 Y Y ++ + P+ Sbjct: 304 YEY-LRSLEPI 313 Score = 36.2 bits (82), Expect = 2e-06 Identities = 32/137 (23%), Positives = 60/137 (43%), Gaps = 13/137 (9%) Query: 169 GSDPVISRGAYLVEGLGHCGACHTPRALTM----QEKALSASGGSDFLSGSAPLEG-WIA 223 GS I+RG YL + C CH+ R ++ GG F S L G +++ Sbjct: 43 GSTEQIARGEYLANHVMLCMDCHSDRNYSLFSGPPHPGTKGLGGDRF-DRSMGLPGVFVS 101 Query: 224 KSLRGDHKDGLGSWSEEQLVQFLKTG-RSDRSAVFGGMSDVVVHSMQYMTDADLTAIARY 282 ++ +G+G+W++ +L + + TG + + +F M S + D+ A+ Y Sbjct: 102 PNIT---PEGIGNWTDGELYRLITTGVKKNGEPIFPVMP---YQSYGKLDPEDIKAVIAY 155 Query: 283 LKSLPANDPKDQPHQYD 299 +++L P + D Sbjct: 156 IRTLAPQKSNIPPREID 172 Lambda K H 0.316 0.131 0.404 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: 383 Number of extensions: 29 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 434 Length of database: 330 Length adjustment: 30 Effective length of query: 404 Effective length of database: 300 Effective search space: 121200 Effective search space used: 121200 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 (21.6 bits) S2: 50 (23.9 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