Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate HSERO_RS22810 HSERO_RS22810 alcohol dehydrogenase
Query= BRENDA::Q5FRK5 (437 letters) >FitnessBrowser__HerbieS:HSERO_RS22810 Length = 423 Score = 355 bits (911), Expect = e-102 Identities = 182/403 (45%), Positives = 252/403 (62%), Gaps = 18/403 (4%) Query: 20 TAQDSDKAIVEKGRYLAAASDCAACHSVHGKPEYSGGVSFSLPMGKIYSTNITPDPDHGI 79 TAQ +D+ +V +G+YLA A DC ACHS GKP YSGG++ G IYSTNITPD +HGI Sbjct: 23 TAQAADQDLVARGQYLARAGDCMACHSAAGKPAYSGGLAIDSGHGIIYSTNITPDKEHGI 82 Query: 80 GRYTEAQFGQALRQGIRRDGSTLYPAMPFPSYARLTDSDIHALFVYFRDGVKAVPVSAPR 139 G Y+EAQF A+R G+R DG+ LYPAMP+PSYA+++D DIHAL+ YF GV+ V + P Sbjct: 83 GNYSEAQFSAAVRHGVRADGTQLYPAMPYPSYAKVSDEDIHALYTYFMQGVQPVASTPPA 142 Query: 140 NEIPWPLSIRWPLTFWRWAFA-PTPHKAITSTAGEFTDPLLARGAYLVEGPAHCGACHSP 198 + + +P +IRW + W FA P + + E + RGAYLVEG HCG+CH+P Sbjct: 143 SSMSFPFNIRWGMKLWNVFFANDKPFREQDGWSAE-----IKRGAYLVEGLGHCGSCHTP 197 Query: 199 RAITMQEKALIAHDGSLYLAGGAPVDGWTPPSLRQENRTGLGRWSEEDIVSFLRTGRSNP 258 R + M EKA + +L+GG ++GW PSLR G+ WS +DIV +L+TGR+ Sbjct: 198 RGVAMNEKASDSSQAQ-FLSGG-DLNGWAVPSLR-----GMPHWSAQDIVDYLQTGRNKT 250 Query: 259 GSVFGSMTSAVLHGTQKLTDNDLHAIAHYLKSLPPADRTQT----PWTYDPTITDQLHKA 314 SV G M+ V H T L DL A+A YLK+L P + + P D T++ Sbjct: 251 ASVAGEMSLVVEHSTSHLKREDLQAMAAYLKTLSPVASSGSGRVIPQGVDATVSKLTAAK 310 Query: 315 DLSSRGARIYVDRCAACHRTDGKGYPAVFPPLAGNSVMMQSDPVSLVHIVQKGASLPAMT 374 DL + G R+Y+D CAACH G+G P +FP L G +V+ +P +L+H++ GA P+ Sbjct: 311 DL-TLGERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAENPSALLHVILAGARTPSTE 369 Query: 375 AAPSSITMPAFSHKLTDQQIADVVTFIRHAWGNNASPVSAEDV 417 APS + MP F+H+L+D++ A + TF+R WGN+A VS +V Sbjct: 370 KAPSILVMPGFAHRLSDEEAAALATFVRQGWGNHAGKVSEREV 412 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: 587 Number of extensions: 28 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: 437 Length of database: 423 Length adjustment: 32 Effective length of query: 405 Effective length of database: 391 Effective search space: 158355 Effective search space used: 158355 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: 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