Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate WP_062057113.1 N456_RS11775 NADP-specific glutamate dehydrogenase
Query= curated2:B2RKJ1 (445 letters) >NCBI__GCF_001401755.1:WP_062057113.1 Length = 447 Score = 530 bits (1365), Expect = e-155 Identities = 258/444 (58%), Positives = 332/444 (74%), Gaps = 2/444 (0%) Query: 2 KTQEIMTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRV 61 K M + A++ E EFLQAV+EV +V ++ + I+ R+VEP+R FRV Sbjct: 4 KIDAFMEEVRARNAHEPEFLQAVQEVAETVIPYIAKNEIYNGKNILLRMVEPERAIMFRV 63 Query: 62 PWVDDQGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMG 121 PWVDD+G++ VN GYR+Q N+AIGPYKGG+RFHPSVN+SILKFL FEQ+FKN+LTTLPMG Sbjct: 64 PWVDDKGEIHVNRGYRIQMNSAIGPYKGGLRFHPSVNISILKFLAFEQVFKNSLTTLPMG 123 Query: 122 GGKGGADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKK 181 GGKGG+DF PKGKS+ EIMRFC SFM+EL+R+IGPDTD+PAGDIGVGGRE+G++FGMY+K Sbjct: 124 GGKGGSDFDPKGKSDDEIMRFCHSFMSELFRHIGPDTDVPAGDIGVGGREIGFLFGMYRK 183 Query: 182 LAREHTGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAW 241 + E TG LTGKG +GGS +RPE+TG+G VYF +NM + G + GK + ISG GNVA Sbjct: 184 MRNEFTGVLTGKGLTWGGSLIRPEATGYGTVYFAKNMLETKGESFDGKIVTISGSGNVAQ 243 Query: 242 GVAQKATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQ 301 A+KAT+LG K+VT+S GY+YD DGI+ EK +++L++ +S+Y ++P+A+ Sbjct: 244 YAAEKATQLGGKIVTLSDSSGYIYDADGIDA-EKLAFVMELKNIKRGRISEYATKYPSAE 302 Query: 302 FFPGKKPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANK 361 F GK PWE K D A+PCATQNE++ +DA TL NG ++E +NM T EA + K Sbjct: 303 FHQGKTPWEVKCDIALPCATQNELDGDDAATLIANGCVCISEGANMPSTPEAIAAFHKAK 362 Query: 362 MLFAPGKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKDGN-Y 420 + FAPGKA NAGGV+ SGLEMTQN++ WT EEVD L QIM+DIH C+ YG D + Y Sbjct: 363 IFFAPGKASNAGGVATSGLEMTQNSLRYNWTREEVDDKLKQIMEDIHSACLEYGTDDDGY 422 Query: 421 IDYVKGANIAGFMKVAKAMVAQGV 444 +DYVKGANIAGF+KVA AM+AQGV Sbjct: 423 VDYVKGANIAGFVKVADAMLAQGV 446 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: 711 Number of extensions: 27 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: 445 Length of database: 447 Length adjustment: 32 Effective length of query: 413 Effective length of database: 415 Effective search space: 171395 Effective search space used: 171395 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 24 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