Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate HSERO_RS19260 HSERO_RS19260 glutamate dehydrogenase
Query= BRENDA::P27346 (421 letters) >FitnessBrowser__HerbieS:HSERO_RS19260 Length = 430 Score = 389 bits (999), Expect = e-113 Identities = 191/408 (46%), Positives = 273/408 (66%), Gaps = 6/408 (1%) Query: 15 QVKNACDKLGMEPAVYELLKEPMRVIEVSIPVKMDDGSIKTFKGFRSQHNDAVGPTKGGI 74 Q+ LG E LK P R++ V +P++ DDG+I F+G+R QHN + GP KGG+ Sbjct: 27 QIDRVTPYLGSLARWVETLKRPKRMLVVDVPIERDDGTIAHFEGYRVQHNTSRGPGKGGV 86 Query: 75 RFHQNVSRDEVKALSIWMTFKCSVTGIPYGGGKGGIIVDPSTLSQGELERLSRGYIDGIY 134 RFHQ+V+ EV ALS WMT K + +PYGG KGGI VDP TLS+GEL+R++R Y I Sbjct: 87 RFHQDVTLSEVMALSAWMTIKNAAVNVPYGGAKGGIRVDPKTLSRGELQRVTRRYTSEIG 146 Query: 135 KLIGEKVDVPAPDVNTNGQIMSWMVDEYNKLTGQSSIGVITGKPVEFGGSLGRTAATGFG 194 +IG D+PAPDVNT+ QIM+WM+D Y+ G +S GV+TGKP+ GGSLGR ATG G Sbjct: 147 IIIGPNKDIPAPDVNTDSQIMAWMMDTYSMNQGSTSSGVVTGKPISLGGSLGRHEATGRG 206 Query: 195 VAVTAREAAAKLGIDMKKAKIAVQGIGNVGSYTVLNCEKLGGTVVAMAEWCKSEGSYAIY 254 V V EAAAK G+D+K AK+AVQG GNVG + G VVA+ + + ++ Sbjct: 207 VFVVGCEAAAKRGLDIKDAKVAVQGFGNVGGIAARLFAEAGSKVVAVQDHVTT-----VF 261 Query: 255 NENGLDGQAMLDYMKEHGNLLNFPGAKRIS-LEEFWASDVDIVIPAALENSITKEVAESI 313 N GLD A+ Y+ ++G++ F GA I+ +FW+ D DI++PAALE IT+ A I Sbjct: 262 NAGGLDVPALQAYVAKNGSVKGFAGADEITDRAQFWSVDCDILVPAALEQQITEANANQI 321 Query: 314 KAKLVCEAANGPTTPEADEVFAERGIVLTPDILTNAGGVTVSYFEWVQNLYGYYWSEEEV 373 KAK++ E ANGPTTP AD++ ++G+++ PD++ NAGGVTVSYFEWVQ+ ++W+E+E+ Sbjct: 322 KAKIILEGANGPTTPAADDILRDKGVLIVPDVIANAGGVTVSYFEWVQDFSSFFWTEDEI 381 Query: 374 EQKEEIAMVKAFESIWKIKEEYNVTMREAAYMHSIKKVAEAMKLRGWY 421 + M +AF ++W++ +E V++R AA++ + +V +A ++RG Y Sbjct: 382 NLRLTRIMREAFAAVWQLADEKKVSLRTAAFIVACTRVLQAREMRGLY 429 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: 477 Number of extensions: 17 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: 421 Length of database: 430 Length adjustment: 32 Effective length of query: 389 Effective length of database: 398 Effective search space: 154822 Effective search space used: 154822 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