Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate WP_097030654.1 CRO07_RS10535 c-type cytochrome
Query= BRENDA::Q5FRK5 (437 letters) >NCBI__GCF_900207575.1:WP_097030654.1 Length = 547 Score = 156 bits (394), Expect = 2e-42 Identities = 101/284 (35%), Positives = 141/284 (49%), Gaps = 18/284 (6%) Query: 23 DSDKAIVEKGRYLAAASDCAACHSVHGKPEYS---GGVSFSLPMGKIYSTNITPDPDHGI 79 D+ A ++ G+ + A DCA CH+ G+P+ + GG G+ + NI+PD GI Sbjct: 47 DAGPADLDNGQRIFLAGDCATCHATPGQPDQTKLGGGRVLDTAFGRFHMPNISPDRVDGI 106 Query: 80 GRYTEAQFGQALRQG-----IRRDGSTLYPAMPFPSYARLTDSDIHALFVYFRDGVKAVP 134 G +T QF +A+R+G I DG LYP+ P+ SY RL +D+ ++ Y + V Sbjct: 107 GGWTLEQFTRAVREGVGPGGIMPDGQNLYPSFPYTSYQRLNANDVRDMYAYIMS-LPPVA 165 Query: 135 VSAPRNEIPWPLSIRWPLTFWRWAFA---PTPHKAITSTAGEFTDPLLARGAYLVEGPAH 191 P +E+ +P +IR + WR AF P P T TA + +LARG YLVEG H Sbjct: 166 GQVPGHELKFPYNIRRGIGVWRLAFLDGQPLPDAPATQTAPDPHQAVLARGRYLVEGAGH 225 Query: 192 CGACHSPRAITMQEKALIAHDGSLYLAGGAPVDGWTPPSLRQENRTGLGRWSEEDIVSFL 251 C CHSPR+ A S Y GG DG + TG+G WS I ++L Sbjct: 226 CAECHSPRSFMGNVIA-----DSRY-GGGPTPDGHGHFPNISPDETGIGFWSVNAIANYL 279 Query: 252 RTGRSNPGSVFGSMTSAVLHGTQKLTDNDLHAIAHYLKSLPPAD 295 TG S G G V+ T +L D A+A YLK++P D Sbjct: 280 ETGISPIGKKAGGDMEEVILNTAQLPREDRLAMAMYLKTVPAVD 323 Score = 41.6 bits (96), Expect = 6e-08 Identities = 46/140 (32%), Positives = 61/140 (43%), Gaps = 19/140 (13%) Query: 17 AEATAQDSDKAIVEKGRYLA-AASDCAACHS-------VHGKPEYSGGVSFSLPMGKIYS 68 A TA D +A++ +GRYL A CA CHS V Y GG + P G + Sbjct: 201 ATQTAPDPHQAVLARGRYLVEGAGHCAECHSPRSFMGNVIADSRYGGGPT---PDGHGHF 257 Query: 69 TNITPDPDHGIGRYTEAQFGQALRQGIRRDGSTLYPAMP--FPSYARLTDSDIHALFVYF 126 NI+PD + GIG ++ L GI G M + A+L D A+ +Y Sbjct: 258 PNISPD-ETGIGFWSVNAIANYLETGISPIGKKAGGDMEEVILNTAQLPREDRLAMAMY- 315 Query: 127 RDGVKAVP-VSAPRNEIPWP 145 +K VP V AP P P Sbjct: 316 ---LKTVPAVDAPGPGRPEP 332 Lambda K H 0.319 0.133 0.420 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: 787 Number of extensions: 52 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 437 Length of database: 547 Length adjustment: 34 Effective length of query: 403 Effective length of database: 513 Effective search space: 206739 Effective search space used: 206739 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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