Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_012468656.1 GLOV_RS02780 NADP-specific glutamate dehydrogenase
Query= BRENDA::Q9TVN3 (438 letters) >NCBI__GCF_000020385.1:WP_012468656.1 Length = 448 Score = 473 bits (1218), Expect = e-138 Identities = 240/437 (54%), Positives = 310/437 (70%), Gaps = 6/437 (1%) Query: 3 DLEARNPAQPEFIQASREVIESIIDVVNSNPKYLENKILERITEPNLIHEFKVEWENDKH 62 D+ RNP + EF QA EV+ES+ VV +P+YLE KI+ERI EP F+V W++DK Sbjct: 14 DVLKRNPGEIEFHQAVLEVLESLGPVVVKHPEYLERKIIERICEPERQIIFRVPWQDDKG 73 Query: 63 EIMVNKGYRIQFNNAIGPYKGGLRFHRAVTLGTLKFLGFEQIFKNSLTGLPMGGGKGGSD 122 ++ +N+G+R++FN+++GPYKGGLRFH +V LG +KFLGFEQIFKNSLTGLP+GGGKGGSD Sbjct: 74 QVHINRGFRVEFNSSLGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGLPIGGGKGGSD 133 Query: 123 FDPRGKSDAEILRFCRSFMTSLFKYIGPEIDVPAGDIGVGGREIGYLFGQYKRLTQQHE- 181 FDP+GKSD E++RFC+SFMT L++++G DVPAGDIGVGGREIGY+FGQYKR+T ++E Sbjct: 134 FDPKGKSDDEVMRFCQSFMTELYRHLGEHTDVPAGDIGVGGREIGYMFGQYKRITNRYEP 193 Query: 182 GVLTGKGLNWGGSLVRPEATGFGTMYFANEVLHAHGDDIKGKTIAISGFGNVAFGAVLKA 241 GVLTGKGL WGGSLVR EATG+G YF NE L D +GKT +SG GNVA + K Sbjct: 194 GVLTGKGLTWGGSLVRTEATGYGATYFINEALKVRKDTFEGKTCLVSGSGNVAIYTIEKI 253 Query: 242 KQLGAKVVTISGPDGYIYDENGINTDEKINYMLELRASNNDVVAPFA-EKFGAKFIPGKK 300 QLG K V S +G IY E G++ D + +L+ ++ +A AK+IP Sbjct: 254 HQLGGKCVACSDSNGVIYHEKGLDLD----LIKQLKEVERRRISDYALAHKDAKYIPNGN 309 Query: 301 PWEVPVDMAFPCAIQNELNAEDAATLHKNGVKYVIETSNMGCTADAVQYFIKNRIVFAPG 360 W++P +A P A QNE+N +DAA L KNG V E +NM T + V+ F+ +I + PG Sbjct: 310 IWDIPCQVAMPSATQNEINGKDAAKLVKNGCIAVGEGANMPTTPEGVKVFLDAKIAYGPG 369 Query: 361 KAANAGGVAVSGLEMSQNSMKLNWTAEEVDAKLKNIMTNIHASCVKEGKESDGYINYVKG 420 KAANAGGVA S LEM QN+ + +WT E+ +AKL+NIM NIHA+C + +E NYV G Sbjct: 370 KAANAGGVATSALEMQQNAQRDSWTFEDTEAKLENIMKNIHANCYETAEEYGAPGNYVLG 429 Query: 421 ANIAGFKKVADAMVDLG 437 ANI GF KVA+AMV G Sbjct: 430 ANICGFIKVANAMVAHG 446 Lambda K H 0.317 0.137 0.405 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: 28 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: 438 Length of database: 448 Length adjustment: 32 Effective length of query: 406 Effective length of database: 416 Effective search space: 168896 Effective search space used: 168896 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