Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_062735050.1 AYX06_RS06345 NADP-specific glutamate dehydrogenase
Query= BRENDA::P24295 (450 letters) >NCBI__GCF_001580365.1:WP_062735050.1 Length = 446 Score = 454 bits (1167), Expect = e-132 Identities = 229/432 (53%), Positives = 298/432 (68%), Gaps = 7/432 (1%) Query: 19 EPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGY 78 E EF Q V+EV SLGPVV HPE+ + A+LER+ PER I FRVPW DD G+VH+N G+ Sbjct: 19 EVEFHQAVDEVFDSLGPVVARHPEFLDAAVLERICEPERQIIFRVPWTDDEGRVHINRGF 78 Query: 79 RVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSD 138 RV+FN A+GPYKGGLRF PSV L I+KFLGFEQ FK++LT +P+GG KGGSDFDP+G+SD Sbjct: 79 RVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNALTGMPIGGGKGGSDFDPSGRSD 138 Query: 139 REVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKAR 198 E+MRFCQ+FMTELYRHIG DVPAGD+GVG REIGY++GQY++I + +GVLTGK Sbjct: 139 AEIMRFCQSFMTELYRHIGEYTDVPAGDIGVGGREIGYLFGQYKRITNRYESGVLTGKGL 198 Query: 199 SFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAV 258 S+GGSLVR EATGYG+V + E +++ + G+TV ++G GNVA A + LGA + Sbjct: 199 SWGGSLVRTEATGYGTVMFAEEMLRTRGQSFDGQTVLVSGSGNVATFAIARAQHLGATVI 258 Query: 259 TLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFG--VQFFPGEKPWGQKVD 316 T S G + DP+GI E + +++ R ++ +YA++ G +F W Sbjct: 259 TASDSGGCVVDPDGIDLE----LLRQIKEVERGRISEYAERRGGRARFIAKGSVWDVPGT 314 Query: 317 IIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAG 376 + +PCATQN++D AKK++A+ V E ANMP+T EA R + Q+ ++ P KA NAG Sbjct: 315 VALPCATQNELDGSHAKKLLAHGVVAVAEGANMPSTGEATR-MFQEAGVLFGPGKAANAG 373 Query: 377 GVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGF 436 GV S EM QN+ R SWT + +L Q+MT IHD A AE YG+ N VAGANI GF Sbjct: 374 GVATSALEMQQNASRDSWTFGYTEERLGQIMTSIHDRCAETAEDYGMPGNYVAGANIAGF 433 Query: 437 QKIADAMMAQGI 448 K+A AMMAQG+ Sbjct: 434 VKVAGAMMAQGL 445 Lambda K H 0.317 0.136 0.399 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: 616 Number of extensions: 22 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: 450 Length of database: 446 Length adjustment: 33 Effective length of query: 417 Effective length of database: 413 Effective search space: 172221 Effective search space used: 172221 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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