Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate WP_009123266.1 BUB52_RS02110 NADP-specific glutamate dehydrogenase
Query= curated2:B2RKJ1 (445 letters) >NCBI__GCF_900129655.1:WP_009123266.1 Length = 445 Score = 557 bits (1435), Expect = e-163 Identities = 270/445 (60%), Positives = 343/445 (77%), Gaps = 2/445 (0%) Query: 1 MKTQEIMTMLEAKHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFR 60 M +++ L+ + P E E+ QAV+EVL ++EE YN+HPEF+K +IER+ PDRV+ FR Sbjct: 1 MNAAKVLEDLKRRFPNEPEYHQAVEEVLSTIEEEYNKHPEFDKANLIERLCIPDRVYQFR 60 Query: 61 VPWVDDQGKVQVNIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPM 120 V WVDD+G VQ N+GYRVQ NNAIGPYKGGIRFH SVNLSILKFL FEQ FKN+LTTLPM Sbjct: 61 VTWVDDKGNVQTNMGYRVQHNNAIGPYKGGIRFHASVNLSILKFLAFEQTFKNSLTTLPM 120 Query: 121 GGGKGGADFSPKGKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYK 180 GGGKGG+DFSP+GKS AE+MRF Q+FM ELWR+IGP+TD+PAGDIGVGGREVG+MFGMYK Sbjct: 121 GGGKGGSDFSPRGKSNAEVMRFVQAFMLELWRHIGPETDVPAGDIGVGGREVGFMFGMYK 180 Query: 181 KLAREHTGTLTGKGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVA 240 KL E TGT TGKG EFGGS +RPE+TG+G +YF+ M K G D KGKT ISG GNVA Sbjct: 181 KLTHEFTGTFTGKGREFGGSLIRPEATGYGNIYFLLEMLKTKGTDLKGKTCLISGSGNVA 240 Query: 241 WGVAQKATELGIKVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNA 300 A+K E+G KV+T+S DGY+YDP GI+ EK +++L++ + +Y +++P Sbjct: 241 QYTAEKVLEMGGKVLTMSDSDGYIYDPAGIDR-EKLDYIMELKNLYRGRIREYAEQYPGV 299 Query: 301 QFFPGKKPWEQKVDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVAN 360 ++ G +PW +K D A+P ATQNE+N +DA+ L NGV V+E +NM T EA + + Sbjct: 300 KYVEGARPWSEKADIALPSATQNEINGDDARKLIANGVMAVSEGANMPSTPEAIKVFQEA 359 Query: 361 KMLFAPGKAVNAGGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGKDGN- 419 K+L+APGKA NAGGVS SGLEMTQN++ L W++EEVD+ L IM++IH CV YG + N Sbjct: 360 KILYAPGKAANAGGVSVSGLEMTQNSIKLGWSSEEVDEKLKSIMKNIHAACVQYGTEENG 419 Query: 420 YIDYVKGANIAGFMKVAKAMVAQGV 444 Y++YVKGAN+AGFMKVAKAM+AQG+ Sbjct: 420 YVNYVKGANVAGFMKVAKAMMAQGI 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: 724 Number of extensions: 40 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: 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 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