Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate BWI76_RS13195 BWI76_RS13195 glutamate dehydrogenase
Query= BRENDA::P27346 (421 letters) >FitnessBrowser__Koxy:BWI76_RS13195 Length = 424 Score = 394 bits (1011), Expect = e-114 Identities = 198/407 (48%), Positives = 271/407 (66%), Gaps = 5/407 (1%) Query: 15 QVKNACDKLGMEPAVYELLKEPMRVIEVSIPVKMDDGSIKTFKGFRSQHNDAVGPTKGGI 74 Q+ LG E L+ P R + V IPV+MDDG+I+ F+G+R QHN + GP KGG+ Sbjct: 21 QIDRVAPYLGDLAFWIETLRHPKRALIVDIPVQMDDGTIRHFEGYRVQHNLSRGPGKGGV 80 Query: 75 RFHQNVSRDEVKALSIWMTFKCSVTGIPYGGGKGGIIVDPSTLSQGELERLSRGYIDGIY 134 R+H +V +EV ALS WMT KC+ IPYGG KGGI VDP +LS+GELERL+R Y I Sbjct: 81 RYHPDVDLNEVMALSAWMTIKCAAVNIPYGGAKGGIRVDPFSLSEGELERLTRRYTSEIG 140 Query: 135 KLIGEKVDVPAPDVNTNGQIMSWMVDEYNKLTGQSSIGVITGKPVEFGGSLGRTAATGFG 194 +IG + D+PAPDV TNG++M+WM+D Y+ G + GV+TGKP+ GGSLGR ATG G Sbjct: 141 IIIGPQKDIPAPDVGTNGKVMAWMMDTYSMNHGTTITGVVTGKPIHLGGSLGREKATGRG 200 Query: 195 VAVTAREAAAKLGIDMKKAKIAVQGIGNVGSYTVLNCEKLGGTVVAMAEWCKSEGSYAIY 254 V VT RE A + GI+++ AK+A+QG GNVGS +G +V + + + +Y Sbjct: 201 VFVTGREVARRSGIEIEGAKVALQGFGNVGSEAARLFAGVGARIVVI-----QDHTATLY 255 Query: 255 NENGLDGQAMLDYMKEHGNLLNFPGAKRISLEEFWASDVDIVIPAALENSITKEVAESIK 314 NE G+D A+ + E+ + FPGA+ I+ E FW + +DI+IPAALE IT+E AE++ Sbjct: 256 NEGGIDMAALTAWQAENKQIAGFPGAREIAKEAFWTTPMDILIPAALEGQITRERAETLS 315 Query: 315 AKLVCEAANGPTTPEADEVFAERGIVLTPDILTNAGGVTVSYFEWVQNLYGYYWSEEEVE 374 KLV E ANGPT PEAD+V AERGIV+ PD++ NAGGVTVSYFEWVQ++ ++WSEEE+ Sbjct: 316 CKLVLEGANGPTYPEADDVLAERGIVVVPDVICNAGGVTVSYFEWVQDMASFFWSEEEIN 375 Query: 375 QKEEIAMVKAFESIWKIKEEYNVTMREAAYMHSIKKVAEAMKLRGWY 421 K + M A +++ E ++R AAY+ + +++ A K RG Y Sbjct: 376 AKMDRIMTDAIVHVYEKAVEKACSLRTAAYIVACERILMARKDRGIY 422 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: 475 Number of extensions: 14 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: 424 Length adjustment: 32 Effective length of query: 389 Effective length of database: 392 Effective search space: 152488 Effective search space used: 152488 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: 50 (23.9 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