Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate PfGW456L13_1455 NADP-specific glutamate dehydrogenase (EC 1.4.1.4)
Query= curated2:B2RKJ1 (445 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1455 Length = 445 Score = 501 bits (1291), Expect = e-146 Identities = 244/441 (55%), Positives = 323/441 (73%), Gaps = 2/441 (0%) Query: 4 QEIMTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRVPW 63 + + L+ + P + EF QAV+EVL ++ +P + +GI+ERI EP+R FRV W Sbjct: 6 ESFLARLKKRDPDQPEFHQAVEEVLRTLWPFLEANPHYLTSGILERICEPERAVVFRVSW 65 Query: 64 VDDQGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMGGG 123 VDDQGKVQVN G+R+Q N+AIGPYKGG+RFHPSVN+ +LKFL FEQ FKN+LT+LPMGGG Sbjct: 66 VDDQGKVQVNRGFRIQMNSAIGPYKGGLRFHPSVNMGVLKFLAFEQTFKNSLTSLPMGGG 125 Query: 124 KGGADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKKLA 183 KGG+DF PKGKS+AE+MRFCQ+FM+EL+R+IG D D+PAGDIGVG RE+G++FG YK+L+ Sbjct: 126 KGGSDFDPKGKSDAEVMRFCQAFMSELYRHIGADVDVPAGDIGVGAREIGFLFGQYKRLS 185 Query: 184 REHTGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAWGV 243 + T LTGKG +GGS +RPE+TGFG VYF + M K+ G+ +GK +AISG GNVA Sbjct: 186 NQFTSVLTGKGPSYGGSLIRPEATGFGCVYFAEEMLKRRGLAVEGKRVAISGSGNVAQYA 245 Query: 244 AQKATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQFF 303 A+K +LG KV+++S +G +Y G+ T E++ +L+L++ + + RF +F Sbjct: 246 ARKVMDLGGKVISLSDSEGTLYCESGL-TEEQWLAVLELKNVQRGRIRELADRF-GLEFR 303 Query: 304 PGKKPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANKML 363 G+ PW D A+PCATQNE++ E A+TL +NG VAE +NM T EA + ++ +L Sbjct: 304 AGELPWSLSCDIALPCATQNELDAEAARTLLRNGCICVAEGANMPTTLEAVDLFIEANIL 363 Query: 364 FAPGKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKDGNYIDY 423 FAPGKA NAGGV+ SGLEM+QNAM L WT EVD LH IMQ IH CV YG++ ++Y Sbjct: 364 FAPGKASNAGGVAVSGLEMSQNAMRLAWTGGEVDSKLHAIMQSIHHACVHYGEENGRVNY 423 Query: 424 VKGANIAGFMKVAKAMVAQGV 444 VKGANIAGF+KVA AM+AQGV Sbjct: 424 VKGANIAGFVKVADAMLAQGV 444 Lambda K H 0.319 0.137 0.417 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: 656 Number of extensions: 28 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: 445 Length of database: 445 Length adjustment: 32 Effective length of query: 413 Effective length of database: 413 Effective search space: 170569 Effective search space used: 170569 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: 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