Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate HSERO_RS22385 HSERO_RS22385 GMC family oxidoreductase
Query= BRENDA::A4PIB0 (593 letters) >FitnessBrowser__HerbieS:HSERO_RS22385 Length = 593 Score = 796 bits (2055), Expect = 0.0 Identities = 376/593 (63%), Positives = 442/593 (74%), Gaps = 1/593 (0%) Query: 2 MVSRNEKHTDVVIVGFGWVGAIMARELTQAGLNVVALERGPRRDTWPEGAYPSSIDELTH 61 M ++N K DVVIVGFGW GAIMA+E+T+AG VVALERG RDT+P+GAYP +I+EL + Sbjct: 1 MANKNMKPVDVVIVGFGWTGAIMAKEMTEAGQRVVALERGVYRDTYPDGAYPKTINELEY 60 Query: 62 NTRHALFLQPSQSTVTVRHRDSDVAAPYRQLAAFLPGTGVGGAGLHWSGCHWRISPVELR 121 R LF ++S+ T R + D A PYRQ+A F PG GVGGAGLHWSGCHWRI P ELR Sbjct: 61 QQRFKLFQNLNKSSFTFRRKTGDSAIPYRQIAMFKPGEGVGGAGLHWSGCHWRILPEELR 120 Query: 122 LRSHYEERYGKDFIPQDMTIQDWGVSYEELEPHFAFAESVFGTSGQAYKVNGKIVGD-GN 180 +RSHYEERYGK+FIP+DMT+QDWGVSYEELEP+F FAE + GTSG AY+V GK+V + GN Sbjct: 121 MRSHYEERYGKNFIPKDMTLQDWGVSYEELEPYFDFAEKMMGTSGTAYRVGGKVVDESGN 180 Query: 181 PFDADRSTPFPLPAMKNTYSAELYSKAAAECGYHPFRIPSANASQAYTNPYGCQMGACTF 240 PF+ADRS FPLPA K Y A L+ KAA + G HPF +PSANA+ Y N YGCQMG CTF Sbjct: 181 PFEADRSDNFPLPAQKEQYQAALFRKAAQQAGLHPFTLPSANAAAPYVNQYGCQMGPCTF 240 Query: 241 CGFCSGYACYNYSKASPNVNILPALERESRFELRVECDVLKVETDSSGKKATGVIYRTSK 300 CGFCSGYACYNYSKASPNVNI+PAL + + FELR C+VL++E DSS KKATGV Y Sbjct: 241 CGFCSGYACYNYSKASPNVNIMPALRQSNLFELRSSCNVLRIELDSSRKKATGVTYVDIN 300 Query: 301 GEEVRQTADIVILASFAYNNPYLLLLSGIGQPYDPKTGEGTVGRNFVYQNESGVTLFFGQ 360 G+ V Q A IVI ++FAYNN L LLSGIG+PYDP + G VGRN +Q S + FF Sbjct: 301 GDTVFQPASIVIASTFAYNNARLFLLSGIGKPYDPVSNTGAVGRNIAFQMMSTINAFFEP 360 Query: 361 DKFTNPFIGAGGNGVAIDDFNADNFDHGPLGFVGGAPIWVNQAGSKPISSATVPKGTPQW 420 K N FIGAGGNGVA+DDFN D+ DHGPLGFVGG+PIW N +GSKPIS VP GTP+W Sbjct: 361 GKNINGFIGAGGNGVAVDDFNGDHMDHGPLGFVGGSPIWCNPSGSKPISGIAVPSGTPRW 420 Query: 421 GAHWKKAVKDSFQHTISIHAHGTNMAFRDCYLSLDPTYSDTAGRPLLRITFNWHDNDVKM 480 G WK+AVKDS+ +T+S HG NM +RD Y+ LDP Y D G+PLLR TF+W DND++M Sbjct: 421 GRAWKQAVKDSYLNTMSFDVHGANMVYRDVYVDLDPNYKDAFGQPLLRFTFDWKDNDIRM 480 Query: 481 IRYVTDRMADIGRAMKPESMSVETKEFGEEFDLRHYQTTHIAGGAIMGTSPKDSVVNRYL 540 RYVTD+ I +K + V K+FG DLR YQTTH AGG MGT P SVVNRYL Sbjct: 481 SRYVTDQAVKIAHELKAREIKVTVKDFGAAPDLRSYQTTHWAGGVAMGTDPSTSVVNRYL 540 Query: 541 QHWDVSNLFVIGSSAFPQGIGYNPTGIVAALAYWSAKAIRERYLKSPGPMVQA 593 Q WDV N+F +GS F QGIGYNPTG AL YWSA+AIRE+YL P P+VQA Sbjct: 541 QSWDVHNVFAVGSGVFAQGIGYNPTGAAVALTYWSARAIREQYLNDPRPLVQA 593 Lambda K H 0.319 0.135 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: 1238 Number of extensions: 59 Number of successful extensions: 2 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: 593 Length of database: 593 Length adjustment: 37 Effective length of query: 556 Effective length of database: 556 Effective search space: 309136 Effective search space used: 309136 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 (21.7 bits) S2: 53 (25.0 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