Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate BPHYT_RS16705 BPHYT_RS16705 glutamate dehydrogenase
Query= BRENDA::P27346 (421 letters) >FitnessBrowser__BFirm:BPHYT_RS16705 Length = 437 Score = 402 bits (1033), Expect = e-116 Identities = 195/407 (47%), Positives = 279/407 (68%), Gaps = 5/407 (1%) Query: 15 QVKNACDKLGMEPAVYELLKEPMRVIEVSIPVKMDDGSIKTFKGFRSQHNDAVGPTKGGI 74 QV LG E LK P R++ V +P+++D+G++ F+G+R QHN + GP KGG+ Sbjct: 35 QVDRVAPYLGSLSRWLETLKRPKRILIVDVPIELDNGTVAHFEGYRVQHNVSRGPGKGGV 94 Query: 75 RFHQNVSRDEVKALSIWMTFKCSVTGIPYGGGKGGIIVDPSTLSQGELERLSRGYIDGIY 134 R+HQ+V+ EV ALS WM+ K + +PYGG KGGI VDP TLS+GELER++R Y I Sbjct: 95 RYHQDVTLSEVMALSAWMSVKNAAVNVPYGGAKGGIRVDPRTLSRGELERVTRRYTSEIG 154 Query: 135 KLIGEKVDVPAPDVNTNGQIMSWMVDEYNKLTGQSSIGVITGKPVEFGGSLGRTAATGFG 194 +IG D+PAPDVNTN QIM+WM+D Y+ GQ++ GV+TGKP+ GGSLGR ATG G Sbjct: 155 IIIGPNTDIPAPDVNTNEQIMAWMMDTYSMNQGQTATGVVTGKPITLGGSLGRREATGRG 214 Query: 195 VAVTAREAAAKLGIDMKKAKIAVQGIGNVGSYTVLNCEKLGGTVVAMAEWCKSEGSYAIY 254 V VTA EAA ++G+D++ A+IAVQG GNVG ++ G +VA+ + S +Y Sbjct: 215 VFVTASEAARRIGVDIEGARIAVQGFGNVGGIAARLFQEAGSKLVAVQDHTGS-----LY 269 Query: 255 NENGLDGQAMLDYMKEHGNLLNFPGAKRISLEEFWASDVDIVIPAALENSITKEVAESIK 314 G+D A+L+++ + G + FP A ++ EEFW + DI+IPAALEN IT++ A IK Sbjct: 270 KSTGIDAVALLEHVAKTGGVGGFPEADSVTNEEFWTVESDILIPAALENQITEKNASKIK 329 Query: 315 AKLVCEAANGPTTPEADEVFAERGIVLTPDILTNAGGVTVSYFEWVQNLYGYYWSEEEVE 374 K+V E ANGPTT AD++ +RGI++ PD++ NAGGVTVSYFEWVQ+ ++W+E+E+ Sbjct: 330 TKIVVEGANGPTTTAADDILHDRGILVIPDVVANAGGVTVSYFEWVQDFSSFFWTEDEIN 389 Query: 375 QKEEIAMVKAFESIWKIKEEYNVTMREAAYMHSIKKVAEAMKLRGWY 421 Q+ E M +AF ++W++ E V++R AA++ + K++ EA +LRG Y Sbjct: 390 QRLERVMREAFAAVWQVSSEQKVSVRTAAFIVACKRILEARELRGLY 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: 448 Number of extensions: 11 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