Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate H281DRAFT_04271 H281DRAFT_04271 glutamate dehydrogenase (NAD(P)+)
Query= BRENDA::P27346 (421 letters) >FitnessBrowser__Burk376:H281DRAFT_04271 Length = 437 Score = 400 bits (1027), Expect = e-116 Identities = 195/421 (46%), Positives = 283/421 (67%), Gaps = 5/421 (1%) Query: 1 MSGKDVNVFEMAQSQVKNACDKLGMEPAVYELLKEPMRVIEVSIPVKMDDGSIKTFKGFR 60 ++ +D+ + QV LG E LK P R++ V +P+++D+G++ F+G+R Sbjct: 21 LNSEDLGPWGNYLRQVDRVAPYLGSLSRWLETLKRPKRILIVDVPIELDNGTVAHFEGYR 80 Query: 61 SQHNDAVGPTKGGIRFHQNVSRDEVKALSIWMTFKCSVTGIPYGGGKGGIIVDPSTLSQG 120 QHN + GP KGG+R+HQ+V+ EV ALS WM+ K + +PYGG KGGI VDP TLS+G Sbjct: 81 VQHNVSRGPGKGGVRYHQDVTLSEVMALSAWMSVKNAAVNVPYGGAKGGIRVDPRTLSRG 140 Query: 121 ELERLSRGYIDGIYKLIGEKVDVPAPDVNTNGQIMSWMVDEYNKLTGQSSIGVITGKPVE 180 ELER++R Y I +IG D+PAPDVNTN QIM+WM+D Y+ GQ++ GV+TGKP+ Sbjct: 141 ELERMTRRYTSEIGIIIGPNTDIPAPDVNTNEQIMAWMMDTYSMNQGQTATGVVTGKPIT 200 Query: 181 FGGSLGRTAATGFGVAVTAREAAAKLGIDMKKAKIAVQGIGNVGSYTVLNCEKLGGTVVA 240 GGSLGR ATG GV V EAA ++G D++ A+IAVQG GNVG ++ G VVA Sbjct: 201 LGGSLGRREATGRGVFVVGCEAARRIGFDIEGARIAVQGFGNVGGIAARLFQEAGAKVVA 260 Query: 241 MAEWCKSEGSYAIYNENGLDGQAMLDYMKEHGNLLNFPGAKRISLEEFWASDVDIVIPAA 300 + + S +Y G+D A+LD++ + G + FP A ++ EEFW + DI+IPAA Sbjct: 261 VQDHTGS-----LYKSTGIDAVALLDHVAKTGGVGGFPEADAVTNEEFWTVESDILIPAA 315 Query: 301 LENSITKEVAESIKAKLVCEAANGPTTPEADEVFAERGIVLTPDILTNAGGVTVSYFEWV 360 LEN IT++ A IK K+V E ANGPTT AD++ +RGI++ PD++ NAGGVTVSYFEWV Sbjct: 316 LENQITEKNAGKIKTKIVVEGANGPTTTAADDILHDRGILVIPDVVANAGGVTVSYFEWV 375 Query: 361 QNLYGYYWSEEEVEQKEEIAMVKAFESIWKIKEEYNVTMREAAYMHSIKKVAEAMKLRGW 420 Q+ ++W+E+E+ Q+ E M +AF ++W++ E NV++R AA++ + K++ +A ++RG Sbjct: 376 QDFSSFFWTEDEINQRLERVMREAFAAVWQVSSEQNVSVRTAAFIVACKRILQAREMRGL 435 Query: 421 Y 421 Y Sbjct: 436 Y 436 Lambda K H 0.315 0.133 0.390 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: 454 Number of extensions: 10 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: 421 Length of database: 437 Length adjustment: 32 Effective length of query: 389 Effective length of database: 405 Effective search space: 157545 Effective search space used: 157545 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: 42 (22.0 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