Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate Ac3H11_315 NADP-specific glutamate dehydrogenase (EC 1.4.1.4)
Query= curated2:B2RKJ1 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_315 Length = 464 Score = 502 bits (1292), Expect = e-146 Identities = 252/434 (58%), Positives = 317/434 (73%), Gaps = 5/434 (1%) Query: 13 KHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRVPWVDDQGKVQV 72 ++PG+ EFLQAV EV+ S+ +HP + ++G++ER+VEP+R+ FRV WVDD G VQV Sbjct: 33 RNPGQPEFLQAVTEVMESLWPFIAEHPRYAEHGLLERLVEPERIVMFRVSWVDDHGTVQV 92 Query: 73 NIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMGGGKGGADFSPK 132 N GYR+Q + AIGP+KGGIRFHPSVNLS+LKFL FEQ FKNALTTLPMGGGKGG+DF PK Sbjct: 93 NRGYRIQHSMAIGPFKGGIRFHPSVNLSVLKFLAFEQTFKNALTTLPMGGGKGGSDFDPK 152 Query: 133 GKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKKLAREHTGTLTG 192 G+S E+MRFCQ+F++EL+R++G DTD+PAGDIGVGGREVG+M GM KKL+ TG Sbjct: 153 GRSPGEVMRFCQAFVSELFRHVGADTDVPAGDIGVGGREVGFMAGMMKKLSNRADCVFTG 212 Query: 193 KGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAWGVAQKATELGI 252 KG FGGS +RPE+TG+G VYF Q M + NG G +++SG GNVA +KA +LG Sbjct: 213 KGLSFGGSLIRPEATGYGTVYFAQEMLRANGRSLDGLRVSVSGSGNVAQYAVEKALQLGA 272 Query: 253 KVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQFFPGKKPWEQK 312 KV+T+S G + D DG TPEK ++D+++ VSDY +R +F G +PW Sbjct: 273 KVITVSDSSGTIVDEDGF-TPEKLAILMDVKNHHYGRVSDYAER-TGVKFEAGVRPWHVP 330 Query: 313 VDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANKMLFAPGKAVNA 372 VD A+PCATQNE++ DA TL KNGV VAE +NM T EA++ + A +L+APGKA NA Sbjct: 331 VDVALPCATQNELDARDAATLIKNGVVCVAEGANMPSTIEAAKVFEAAGVLYAPGKASNA 390 Query: 373 GGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGK--DGNYIDYVKGANIA 430 GGV+ SGLEM+QNA L W EEVD L QIMQ IH C+ YGK DG + YV GANIA Sbjct: 391 GGVATSGLEMSQNAARLAWPREEVDARLLQIMQGIHAACLRYGKHADGR-VSYVDGANIA 449 Query: 431 GFMKVAKAMVAQGV 444 GF+KVA AM+AQGV Sbjct: 450 GFVKVADAMLAQGV 463 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: 617 Number of extensions: 25 Number of successful extensions: 4 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: 464 Length adjustment: 33 Effective length of query: 412 Effective length of database: 431 Effective search space: 177572 Effective search space used: 177572 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