Align Cryptic catabolic NAD-specific glutamate dehydrogenase GudB; NAD-GDH; EC 1.4.1.2 (characterized)
to candidate RR42_RS02570 RR42_RS02570 glutamate dehydrogenase
Query= SwissProt::P50735 (427 letters) >FitnessBrowser__Cup4G11:RR42_RS02570 Length = 435 Score = 401 bits (1030), Expect = e-116 Identities = 192/386 (49%), Positives = 270/386 (69%), Gaps = 3/386 (0%) Query: 40 ELLKEPMRLLTVKIPVRMDDGSVKIFTGYRAQHNDSVGPTKGGIRFHPNVTEKEVKAVKA 99 E LK P R L V +P+ MD+G++ F GYR QHN S GP KGG+RFH +VT EV A Sbjct: 50 ETLKRPKRALVVDVPIEMDNGTIAHFEGYRVQHNMSRGPGKGGVRFHQDVTLSEVMA--- 106 Query: 100 LSIWMSLKCGIIDLPYGGGKGGIVCDPRDMSFRELERLSRGYVRAISQIVGPTKDVPAPD 159 LS WMS+K +++PYGG KGGI DPR +S ELER++R Y I+ I+GP KD+PAPD Sbjct: 107 LSAWMSVKNAAVNVPYGGAKGGIRVDPRTLSRSELERVTRRYTSEINFIIGPNKDIPAPD 166 Query: 160 VFTNSQIMAWMMDEYSRIDEFNSPGFITGKPLVLGGSHGRESATAKGVTICIKEAAKKRG 219 V TN Q+MAWMMD YS + G +TGKP+ LGGS GR AT +GV + EAA+ G Sbjct: 167 VNTNEQVMAWMMDTYSMNSGSTATGVVTGKPISLGGSLGRREATGRGVFVVGSEAARNLG 226 Query: 220 IDIKGARVVVQGFGNAGSYLAKFMHDAGAKVVGISDAYGGLYDPEGLDIDYLLDRRDSFG 279 ++IKGAR+ VQGFGN G+ AK H+AGAKVV + D LY+P GLD+ +++ G Sbjct: 227 LEIKGARIAVQGFGNVGAVAAKLFHEAGAKVVAVQDHRTALYNPAGLDVPAMMEYASHSG 286 Query: 280 TVTKLFNDTITNQELLELDCDILVPAAIENQITEENAHNIRAKIVVEAANGPTTLEGTKI 339 T+ +TI+ ++ ++DC+IL+PAA+E QIT +NA +I+A++V+E ANGPTT E I Sbjct: 287 TIEGFQGETISAEQFWQVDCEILIPAALEGQITAQNAPHIKARMVIEGANGPTTPEADDI 346 Query: 340 LSDRDILLVPDVLASAGGVTVSYFEWVQNNQGFYWSEEEVEEKLEKMMVKSFNNIYEMAN 399 L +R+IL+ PDV+A+AGGVTVSYFEWVQ+ F+W+EEE+ ++L ++M ++F I+++A Sbjct: 347 LRERNILVAPDVIANAGGVTVSYFEWVQDFSSFFWTEEEINQRLVRIMQEAFRAIWQVAQ 406 Query: 400 NRRIDMRLAAYMVGVRKMAEASRFRG 425 + ++ +R AA++V ++ +A RG Sbjct: 407 DNKVTLRTAAFIVACTRILQAREMRG 432 Lambda K H 0.318 0.136 0.398 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: 476 Number of extensions: 20 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: 427 Length of database: 435 Length adjustment: 32 Effective length of query: 395 Effective length of database: 403 Effective search space: 159185 Effective search space used: 159185 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 (21.7 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