Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate Dsui_3211 Dsui_3211 glutamate dehydrogenase/leucine dehydrogenase
Query= curated2:B2RKJ1 (445 letters) >FitnessBrowser__PS:Dsui_3211 Length = 448 Score = 508 bits (1307), Expect = e-148 Identities = 253/441 (57%), Positives = 324/441 (73%), Gaps = 5/441 (1%) Query: 7 MTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRVPWVDD 66 + L+ + P + EFLQAVKEVL ++ ++P + + G+++RIVEP+R FRVPWVDD Sbjct: 9 LARLQLRDPQQPEFLQAVKEVLETLWPFLQENPRYRRLGLLDRIVEPERAIMFRVPWVDD 68 Query: 67 QGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMGGGKGG 126 G+VQVN GYR+Q ++AIGPYKGGIRFHPSVNLSILKFL FEQ+FKN+LTTLPMGGGKGG Sbjct: 69 AGQVQVNRGYRIQMSSAIGPYKGGIRFHPSVNLSILKFLAFEQVFKNSLTTLPMGGGKGG 128 Query: 127 ADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKKLAREH 186 ADF PKGKS+ E+MRFCQ+FM EL ++IG D D+PAGDIGVGGREVGYMFGMYKKL E Sbjct: 129 ADFDPKGKSDLEVMRFCQAFMAELHKHIGADIDVPAGDIGVGGREVGYMFGMYKKLEGEF 188 Query: 187 TGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAWGVAQK 246 + LTGKG ++GGS +RPE+TG+G +YFV+NM + +G + +SG GNVA AQK Sbjct: 189 SSVLTGKGLDYGGSLIRPEATGYGTIYFVENMLATRNMGLEGLRVTVSGSGNVAQFAAQK 248 Query: 247 ATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQFFPGK 306 A LG KV+++S G V+DPDG+ T EK+ + +++ V DY ++F F PG+ Sbjct: 249 AMRLGAKVISVSDSGGTVHDPDGM-TEEKWSALHHIKEVQRGRVEDYARQF-GLTFLPGQ 306 Query: 307 KPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANKMLFAP 366 +PW D A+PCATQNE++ DA+TL +NGV VAE +NM T EA ++ +L+AP Sbjct: 307 RPWSIPCDVALPCATQNELDGNDARTLLQNGVRCVAEGANMPSTLEAVHAFLEAGILYAP 366 Query: 367 GKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGK---DGNYIDY 423 GKA NAGGV+ SGLEM+QNA+ L WT +EVD+ L QIM IH CV +G I+Y Sbjct: 367 GKASNAGGVAVSGLEMSQNALRLSWTRDEVDQRLKQIMLSIHAACVGHGSGRGQRGSINY 426 Query: 424 VKGANIAGFMKVAKAMVAQGV 444 V GANIAGF+KVA AM+AQGV Sbjct: 427 VAGANIAGFVKVADAMLAQGV 447 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: 682 Number of extensions: 34 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: 448 Length adjustment: 33 Effective length of query: 412 Effective length of database: 415 Effective search space: 170980 Effective search space used: 170980 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