Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate GFF4743 PS417_24260 glutamate dehydrogenase
Query= BRENDA::Q9TVN3 (438 letters) >FitnessBrowser__WCS417:GFF4743 Length = 445 Score = 509 bits (1311), Expect = e-149 Identities = 255/434 (58%), Positives = 328/434 (75%), Gaps = 2/434 (0%) Query: 4 LEARNPAQPEFIQASREVIESIIDVVNSNPKYLENKILERITEPNLIHEFKVEWENDKHE 63 L+ R+P QPEF QA EV+ S+ + +NP YL + ILERI EP F+V W +D + Sbjct: 12 LKKRDPDQPEFHQAVEEVLRSLWPFLEANPHYLTSGILERICEPERAITFRVSWVDDHGK 71 Query: 64 IMVNKGYRIQFNNAIGPYKGGLRFHRAVTLGTLKFLGFEQIFKNSLTGLPMGGGKGGSDF 123 + VN+G+RIQ N+AIGPYKGGLRFH +V LG LKFL FEQ FKNSLT LPMGGGKGGSDF Sbjct: 72 VQVNRGFRIQMNSAIGPYKGGLRFHPSVNLGVLKFLAFEQTFKNSLTSLPMGGGKGGSDF 131 Query: 124 DPRGKSDAEILRFCRSFMTSLFKYIGPEIDVPAGDIGVGGREIGYLFGQYKRLTQQHEGV 183 DP+GKSDAE++RFC++FM+ L+++IG ++DVPAGDIGVG REIG+LFGQYKRL+ Q V Sbjct: 132 DPKGKSDAEVMRFCQAFMSELYRHIGADVDVPAGDIGVGAREIGFLFGQYKRLSNQFTSV 191 Query: 184 LTGKGLNWGGSLVRPEATGFGTMYFANEVLHAHGDDIKGKTIAISGFGNVAFGAVLKAKQ 243 LTGKG+ +GGSL+RPEATGFG +YFA E+L + ++GK +A+SG GNVA A K Sbjct: 192 LTGKGMTYGGSLIRPEATGFGCVYFAEEMLKRNNQRVEGKRVAVSGSGNVAQYAARKVMD 251 Query: 244 LGAKVVTISGPDGYIYDENGINTDEKINYMLELRASNNDVVAPFAEKFGAKFIPGKKPWE 303 LG KV+++S +G +Y E+G+ T+E+ + +LEL+ ++ AE+FG +F G+ PWE Sbjct: 252 LGGKVISLSDSEGTLYAESGL-TEEQWSALLELKNVQRGRISELAERFGLEFRKGQTPWE 310 Query: 304 VPVDMAFPCAIQNELNAEDAATLHKNGVKYVIETSNMGCTADAVQYFIKNRIVFAPGKAA 363 + D+A PCA QNEL+A+ A TL +NG V E +NM T +AV FI+ I+FAPGKA+ Sbjct: 311 LACDIALPCATQNELDADAARTLLRNGCICVAEGANMPTTLEAVDIFIEAGILFAPGKAS 370 Query: 364 NAGGVAVSGLEMSQNSMKLNWTAEEVDAKLKNIMTNIHASCVKEGKESDGYINYVKGANI 423 NAGGVAVSGLEMSQN+M+L WTA EVD+KL NIM +IH +CV G+E +G INYVKGANI Sbjct: 371 NAGGVAVSGLEMSQNAMRLLWTAGEVDSKLHNIMQSIHHACVHYGEE-NGRINYVKGANI 429 Query: 424 AGFKKVADAMVDLG 437 AGF KVADAM+ G Sbjct: 430 AGFVKVADAMLAQG 443 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: 576 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: 445 Length adjustment: 32 Effective length of query: 406 Effective length of database: 413 Effective search space: 167678 Effective search space used: 167678 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 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