Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate RR42_RS33640 RR42_RS33640 glutamate dehydrogenase
Query= curated2:B2RKJ1 (445 letters) >FitnessBrowser__Cup4G11:RR42_RS33640 Length = 447 Score = 488 bits (1256), Expect = e-142 Identities = 237/433 (54%), Positives = 317/433 (73%), Gaps = 3/433 (0%) Query: 13 KHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRVPWVDDQGKVQV 72 + P + EFLQAVKEV++++ QHP + + ++ER+VEP+RV FRV W DD+G+VQV Sbjct: 16 RDPDQPEFLQAVKEVMMTLWPFVEQHPRYGEQALLERLVEPERVIQFRVAWTDDRGQVQV 75 Query: 73 NIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMGGGKGGADFSPK 132 N G+RVQ ++AIGPYKGG+R HP+VNLS+LKFLGFEQ KNALTTLPMGGGKGG+DF PK Sbjct: 76 NRGFRVQHSSAIGPYKGGMRLHPTVNLSVLKFLGFEQTLKNALTTLPMGGGKGGSDFDPK 135 Query: 133 GKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKKLAREHTGTLTG 192 GKS+ E+MRFCQ+ MTEL+R++GPDTD+PAGDIGVG REVG+M GM KKL+ TG Sbjct: 136 GKSDGEVMRFCQALMTELYRHLGPDTDVPAGDIGVGAREVGFMAGMMKKLSNSSASVFTG 195 Query: 193 KGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAWGVAQKATELGI 252 KG FGGS +RPE+TG+G VYF Q M + G D+ G + +SG GNVA A+KA ELG Sbjct: 196 KGMAFGGSLMRPEATGYGTVYFAQEMLHRRGRDFSGLRVLLSGSGNVAQYAAEKAIELGA 255 Query: 253 KVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQFFPGKKPWEQK 312 KV+T+S G ++ P G+N+ E+ ++ ++ ++++ + F G+ PW Sbjct: 256 KVLTVSDSGGVLHYPKGMNS-EQLSALMAFKNEARGRLAEFAAE-QDLHFEAGRTPWHVP 313 Query: 313 VDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANKMLFAPGKAVNA 372 D A+PCATQNE++ DA+ L NGV VAE +NM T +A + ++A ++L+APGKA NA Sbjct: 314 ADVALPCATQNELDGNDAERLLANGVFCVAEGANMPATLDAVDRFLAARILYAPGKASNA 373 Query: 373 GGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYG-KDGNYIDYVKGANIAG 431 GGV+ SGLEM+QNAM + W + EVD+ LH IM+DIH C+ YG K +I+YV+GAN+AG Sbjct: 374 GGVATSGLEMSQNAMRMSWHHAEVDEKLHAIMKDIHGNCIHYGQKADGFINYVEGANVAG 433 Query: 432 FMKVAKAMVAQGV 444 F+KVA AM+AQGV Sbjct: 434 FVKVADAMLAQGV 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: 658 Number of extensions: 25 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 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