Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_040662046.1 ON16_RS10305 NADP-specific glutamate dehydrogenase
Query= BRENDA::P24295 (450 letters) >NCBI__GCF_000307265.1:WP_040662046.1 Length = 450 Score = 617 bits (1592), Expect = 0.0 Identities = 300/449 (66%), Positives = 361/449 (80%), Gaps = 1/449 (0%) Query: 1 MSKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIE 60 M+ Y+ RV+ + K ++EPEF+QTVEEVLSSL PV+DAHPEYE+ ALLER+V PER IE Sbjct: 1 MNAYLARVLEATKAKNSNEPEFLQTVEEVLSSLEPVIDAHPEYEKAALLERIVEPERTIE 60 Query: 61 FRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTL 120 FRV WEDDN VN GYRVQ+NGA+GPYKGG+RF PSVNLSI+KFLGFEQ FKD++T L Sbjct: 61 FRVTWEDDNHNWQVNRGYRVQYNGALGPYKGGIRFDPSVNLSIIKFLGFEQVFKDAMTGL 120 Query: 121 PMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQ 180 P+GGAKGGSDFDP GKSD EVMRFCQAF++ELYRHIG DID PAGDLG G REIGYMYGQ Sbjct: 121 PIGGAKGGSDFDPRGKSDAEVMRFCQAFISELYRHIGQDIDCPAGDLGCGGREIGYMYGQ 180 Query: 181 YRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFG 240 YR++VG G L+GKA GGS++RPEATGYG+VYY+ + H+ ++ GK +A++G+G Sbjct: 181 YRRLVGASEFGALSGKAVCTGGSILRPEATGYGAVYYLVEALAHDGQSIEGKRIAMSGYG 240 Query: 241 NVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKF 300 NV WG KK ELGAK +GPDGYI+DP+G++T+EK+N++LEMRA + YA+KF Sbjct: 241 NVGWGIMKKAKELGAKVTYFAGPDGYIHDPDGVSTDEKLNFILEMRAKDPMHCKPYAEKF 300 Query: 301 GVQFFPGEKPWGQK-VDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFL 359 G +F G+K WG K VDI MP ATQNDV ++ AK I + VKYYIEVANMPTTN+AL FL Sbjct: 301 GCEFVEGKKCWGVKDVDIYMPAATQNDVKMDSAKLIAESGVKYYIEVANMPTTNDALEFL 360 Query: 360 MQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAE 419 +Q +MVVAPSKAVNAGGV VS EM+QN+ERL WTAEEVD KL +M +I+ S +E Sbjct: 361 KEQKHMVVAPSKAVNAGGVSVSELEMAQNAERLYWTAEEVDEKLKGIMKNIYHSSVEVSE 420 Query: 420 RYGLGYNLVAGANIVGFQKIADAMMAQGI 448 RYGLGY+LVAGANIVGFQK+ADAMMAQGI Sbjct: 421 RYGLGYDLVAGANIVGFQKVADAMMAQGI 449 Lambda K H 0.317 0.136 0.399 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: 728 Number of extensions: 33 Number of successful extensions: 2 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: 450 Length of database: 450 Length adjustment: 33 Effective length of query: 417 Effective length of database: 417 Effective search space: 173889 Effective search space used: 173889 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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