Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate GFF3373 Psest_3438 Glutamate dehydrogenase/leucine dehydrogenase
Query= curated2:B2RKJ1 (445 letters) >FitnessBrowser__psRCH2:GFF3373 Length = 445 Score = 503 bits (1294), Expect = e-147 Identities = 244/438 (55%), Positives = 324/438 (73%), Gaps = 2/438 (0%) Query: 7 MTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRVPWVDD 66 + L+ + P + EF QAV+EV+ S+ HP + + GIIER+VEP+R FRVPWVDD Sbjct: 9 LARLKQRDPHQPEFHQAVEEVVRSLWPFLEAHPHYMQAGIIERMVEPERAIIFRVPWVDD 68 Query: 67 QGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMGGGKGG 126 QG+VQVN G+R+Q N+AIGPYKGG+RFHPSVN+ +LKFL FEQ+FKN+LT+LPMGGGKGG Sbjct: 69 QGRVQVNRGFRIQMNSAIGPYKGGLRFHPSVNIGVLKFLAFEQVFKNSLTSLPMGGGKGG 128 Query: 127 ADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKKLAREH 186 +DF+PKGKS+ E+MRFCQSFM+EL+R+IG D D+PAGDIGVGGRE+G++FG YK+L+ + Sbjct: 129 SDFNPKGKSDNEVMRFCQSFMSELYRHIGADLDVPAGDIGVGGREIGFLFGQYKRLSNQF 188 Query: 187 TGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAWGVAQK 246 T LTGKG +GGS +RPE+TG+G VYF + M K ++GK ++ISG GNVA AQK Sbjct: 189 TSVLTGKGLPYGGSLIRPEATGYGCVYFAEEMLKSTHSSFEGKRVSISGSGNVAQYAAQK 248 Query: 247 ATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQFFPGK 306 ELG +V+++S G ++ PDG+ T E++ ++DL++ + + F + + Sbjct: 249 VMELGGRVISLSDSGGTLHFPDGL-TGEQWDYLMDLKNVRRGRLEEMGAHF-GVTYLADQ 306 Query: 307 KPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANKMLFAP 366 +PW D A+PCATQNE++ EDA+ L KNG VAE +NM T EA + ++ +L+AP Sbjct: 307 RPWSLPCDIALPCATQNELDGEDARMLLKNGCVCVAEGANMPSTLEAVDLFLEAGILYAP 366 Query: 367 GKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKDGNYIDYVKG 426 GKA NAGGV+CSGLEM+QNAM L WT EVD LH IMQ IH CV +G++ I+YVKG Sbjct: 367 GKASNAGGVACSGLEMSQNAMRLHWTAGEVDTKLHSIMQSIHHACVAHGEENGRINYVKG 426 Query: 427 ANIAGFMKVAKAMVAQGV 444 ANIAGF+KVA AM+AQGV Sbjct: 427 ANIAGFVKVADAMLAQGV 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: 678 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