Align Gluconate 2-dehydrogenase flavoprotein; GA 2-DH dehydrogenase subunit; GADH dehydrogenase subunit; EC 1.1.99.3 (characterized)
to candidate 3610514 Dshi_3895 Gluconate 2-dehydrogenase (acceptor) (RefSeq)
Query= SwissProt::O34214 (615 letters) >FitnessBrowser__Dino:3610514 Length = 594 Score = 572 bits (1475), Expect = e-167 Identities = 279/592 (47%), Positives = 376/592 (63%), Gaps = 5/592 (0%) Query: 26 LKKVDAVVVGFGWAGAIMAKELTEAGLNVVALERGPHRDTYPDGAYPQSIDELTYNIRKK 85 L K D V+VG GW G A EL AG V LERG HR P+ DEL Y +R Sbjct: 6 LPKTDVVIVGGGWTGLTAAYELAHAGQRCVVLERGHHRHDATSFGSPEEHDELKYALRYG 65 Query: 86 LFQDLSKSTVTIRHDASQTAVPYRQLAAFLPGTGTGGAGLHWSGVHFRVDPVELNLRSHY 145 QD+ K T+T R+ Q A+P R+L +FLPGTG GGAG+HW+G +R P +L +RSHY Sbjct: 66 HMQDVKKETLTFRNSRDQRALPMRRLGSFLPGTGLGGAGIHWNGQIWRPLPSDLEMRSHY 125 Query: 146 EARYGKNFIPEGMTIQDFGVSYNELEPFFDQAEKVFGTSGSAWTIKGKMIGKEKGGNFYA 205 E RYG FIP+ ++IQD+GV+Y+ELEP D EK+ G +G+A ++G+ ++ GGN + Sbjct: 126 EDRYGSQFIPDELSIQDWGVTYDELEPHLDFFEKICGAAGAAGNLRGE---RQVGGNPFE 182 Query: 206 PDRSSDFPLPAQKRTYSAQLFAQAAESVGYHPYDMPSANTSGPYTNTYGAQMGPCNFCGY 265 RS +P PA K+ S F +AAE +G +P+ MPSAN + Y N YGAQ+ PC +CG+ Sbjct: 183 GPRSDGYPNPAMKQPISNTKFGRAAERMGLNPFPMPSANVTQAYENPYGAQLHPCTYCGF 242 Query: 266 CSGYACYMYSKASPNVNILPALRQEPKFELRNNAYVLRVNLTGDKKRATGVTYLDGQGRE 325 C + C ++KA P + + ++ FE+R +A VLRV + D + ATGV YLD G E Sbjct: 243 CERFGCGYFAKADPIICVYDRIKDHENFEIRFDAQVLRVTKSQDGQTATGVIYLDEDGVE 302 Query: 326 VVQPADLVILSAFQFHNVHLMLLSGIGQPYNPITNEGVVGRNFAYQNISTLKALFDKNTT 385 V QPAD V L+A+ NVHLML+SG+G PY+P T +G VGRN++YQ I+ + A FD+ Sbjct: 303 VFQPADTVCLNAYSLWNVHLMLVSGLGTPYDPETRQGTVGRNYSYQTIAAVDAFFDETVQ 362 Query: 386 TNPFIGAGGAGVAVDDFNADNFDHGPYGFVGGSPFWVNQAGTKPVSGLPTPKGTPNWGSQ 445 T+PF+GAG G+ VDDFN DNFDH GFVGG Q +P+S P P+GTP WG++ Sbjct: 363 TDPFMGAGALGIVVDDFNGDNFDHSDLGFVGGGYIACKQYHGRPISYQPVPEGTPPWGAE 422 Query: 446 WKAAVADTYNHHISMDAHGAHQSYRANYLDLDPNYKNVYGQPLLRMTFDWQDNDIRMAQF 505 WKAAV + Y H + HG+ S NYLDLDP + + YG+PLLRMTF++ D D RM+ + Sbjct: 423 WKAAVRENYTRHADLVIHGSSVSTPENYLDLDPTWTDAYGRPLLRMTFNFPDTDRRMSDY 482 Query: 506 MVGKMRKITEAMNPKMIIGGAK--GPGTHFDTTVYQTTHMSGGAIMGEDPKTSAVNRYLQ 563 ++ + +I + M+ + G ++ YQTTH GGA++G DP+TS VNRY Q Sbjct: 483 VMNRAVEIAQEMDNVTSVSSVNLAAEGKNYSIVPYQTTHNVGGAVIGTDPETSVVNRYGQ 542 Query: 564 SWDVPNVFVPGASAFPQGLGYNPTGMVAALTYWSAKAIREQYLKNPGPLVQA 615 WD NVFV GA FPQ LGYNPTG + L YW+ + ++ YL NP PL+ A Sbjct: 543 MWDHHNVFVFGACLFPQNLGYNPTGPLMGLAYWTLEHMKRDYLPNPRPLMDA 594 Lambda K H 0.317 0.135 0.416 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: 1216 Number of extensions: 61 Number of successful extensions: 3 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: 615 Length of database: 594 Length adjustment: 37 Effective length of query: 578 Effective length of database: 557 Effective search space: 321946 Effective search space used: 321946 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: 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