Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate 3610460 Dshi_3841 Glutamate dehydrogenase (NADP(+)) (RefSeq)
Query= BRENDA::Q9TVN3 (438 letters) >FitnessBrowser__Dino:3610460 Length = 447 Score = 401 bits (1031), Expect = e-116 Identities = 208/433 (48%), Positives = 286/433 (66%), Gaps = 4/433 (0%) Query: 6 ARNPA-QPEFIQASREVIESIIDVVNSNPKYLENKILERITEPNLIHEFKVEWENDKHEI 64 A NP +P F A EV + ++ + ++ Y ++L R+ P+ I F+V W +D E+ Sbjct: 16 ATNPDFEPNFYNALAEVAQDVLTIEKNDKAYAAARVLARLAVPDRILSFRVTWADDAGEV 75 Query: 65 MVNKGYRIQFNNAIGPYKGGLRFHRAVTLGTLKFLGFEQIFKNSLTGLPMGGGKGGSDFD 124 VN+ +R+Q +NAIGPYKGGLRFH +VT TLKFLGFEQ FKN+LTGLPMGG KGG+DF+ Sbjct: 76 QVNQAWRVQTSNAIGPYKGGLRFHPSVTQDTLKFLGFEQCFKNALTGLPMGGAKGGADFN 135 Query: 125 PRGKSDAEILRFCRSFMTSLFKYIGPEIDVPAGDIGVGGREIGYLFGQYKRLTQQHEGVL 184 PRG+S EI+RFC++ M + +IGP+ DVPAGDI VG RE+G+LFG +++ G Sbjct: 136 PRGRSRQEIMRFCQALMAQMAPFIGPDQDVPAGDINVGTREVGWLFGAWRQRRGMFGGAF 195 Query: 185 TGKGLNWGGSLVRPEATGFGTMYFANEVLHAHGDDIKGKTIAISGFGNVAFGAVLKAKQL 244 TGKGL++GGS +R EATGFG +YF +L G ++GK + +SG GNVA A KA + Sbjct: 196 TGKGLSFGGSKMRVEATGFGVVYFVACMLAEMGTSLEGKRVLVSGKGNVATHAAQKAVEE 255 Query: 245 GAKVVTISGPDGYIYDENGINTDEKINYMLELRASNNDVVAPFAEKFGAKFIPGKKPWEV 304 GAKV+T+S G + E G+ D I ++ + + D+ AP AE G +++ G+ PW + Sbjct: 256 GAKVLTLSDTGGTLLAEEGLTLD-AIAWVQARKDAGEDIAAPPAE-LGLRYLEGQTPWHI 313 Query: 305 PVDMAFPCAIQNELNAEDAATLHKNGVKYVIETSNMGCTADAVQYFIKNRIVFAPGKAAN 364 P D+A PCA QNEL+ A L NG+ + E +NM T A + I APGKAAN Sbjct: 314 PADIALPCATQNELDQSAAEILRDNGLMLLAEGANMPLTPGASRVMRLAGIAVAPGKAAN 373 Query: 365 AGGVAVSGLEMSQNSMKLNWTAEEVDAKLKNIMTNIHASCVKEGKESDGYINYVKGANIA 424 AGGVAVSGLEM+QN+ +L W+A VD L++IM IH + V EG+ DG I+Y +GANIA Sbjct: 374 AGGVAVSGLEMTQNAQRLTWSAARVDETLRDIMERIHRAVVAEGR-VDGRIDYGRGANIA 432 Query: 425 GFKKVADAMVDLG 437 ++K+ADA+ G Sbjct: 433 AYRKLADAITAQG 445 Lambda K H 0.317 0.137 0.405 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: 517 Number of extensions: 31 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: 438 Length of database: 447 Length adjustment: 32 Effective length of query: 406 Effective length of database: 415 Effective search space: 168490 Effective search space used: 168490 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: 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