Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_011781951.1 MVAN_RS24140 NADP-specific glutamate dehydrogenase
Query= BRENDA::Q9TVN3 (438 letters) >NCBI__GCF_000015305.1:WP_011781951.1 Length = 449 Score = 453 bits (1165), Expect = e-132 Identities = 223/438 (50%), Positives = 304/438 (69%), Gaps = 7/438 (1%) Query: 3 DLEARNPAQPEFIQASREVIESIIDVVNSNPKYLENKILERITEPNLIHEFKVEWENDKH 62 ++ RNP + EF QA EV++S+ VV+ +P Y++ ++ R+ EP F+V W +D Sbjct: 14 EVARRNPGEAEFHQAVYEVLDSLGPVVDKHPDYVDTAVIRRLCEPERQIIFRVPWLDDGG 73 Query: 63 EIMVNKGYRIQFNNAIGPYKGGLRFHRAVTLGTLKFLGFEQIFKNSLTGLPMGGGKGGSD 122 + +N+G+R++FN+A+GP+KGGLRFH +V LG +KFLGFEQIFKNSLTG+P+GGGKGGSD Sbjct: 74 VVQINRGFRVEFNSALGPFKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGMPIGGGKGGSD 133 Query: 123 FDPRGKSDAEILRFCRSFMTSLFKYIGPEIDVPAGDIGVGGREIGYLFGQYKRLTQQHE- 181 FDP+G+SD E++RFC+SFMT L++++G DVPAGDIGVG REIGYLFGQYKR+T ++E Sbjct: 134 FDPKGRSDGEVMRFCQSFMTELYRHLGEYTDVPAGDIGVGMREIGYLFGQYKRITNRYES 193 Query: 182 GVLTGKGLNWGGSLVRPEATGFGTMYFANEVLHAHGDDIKGKTIAISGFGNVAFGAVLKA 241 GV TGKGL WGGS VR EATG+GT++F +E+L + G G+ + +SG GNVA A+ K Sbjct: 194 GVFTGKGLTWGGSQVRTEATGYGTVFFVDEILRSRGQSFDGRQVVVSGSGNVAIYAIEKV 253 Query: 242 KQLGAKVVTISGPDGYIYDENGINTDEKINYMLELRASNNDVVAPFAE--KFGAKFIPGK 299 LG VV S GY++DENGI+ + + E++ + +AE + A + G+ Sbjct: 254 HALGGTVVACSDSSGYVHDENGID----LGLLKEIKELRRGRMTDYAEARRGAAHHVAGR 309 Query: 300 KPWEVPVDMAFPCAIQNELNAEDAATLHKNGVKYVIETSNMGCTADAVQYFIKNRIVFAP 359 WEVP D+A PCA QNE++ DAA L +G + V E +NM CT +AV+ F + + FAP Sbjct: 310 GVWEVPCDIALPCATQNEVSGADAAQLIDSGCRIVAEGANMPCTPEAVKRFEEAGVTFAP 369 Query: 360 GKAANAGGVAVSGLEMSQNSMKLNWTAEEVDAKLKNIMTNIHASCVKEGKESDGYINYVK 419 GKA NAGGVA S LEM QN+ + +WT E+ +A+L IM IH C+ E NY Sbjct: 370 GKAVNAGGVATSALEMQQNASRDSWTFEDTEARLAEIMGRIHDRCLSTADEYGQPGNYAA 429 Query: 420 GANIAGFKKVADAMVDLG 437 GANIAGF +VADAM+ LG Sbjct: 430 GANIAGFIRVADAMLALG 447 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: 538 Number of extensions: 19 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: 449 Length adjustment: 32 Effective length of query: 406 Effective length of database: 417 Effective search space: 169302 Effective search space used: 169302 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