Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate CA265_RS03475 CA265_RS03475 glutamate dehydrogenase
Query= BRENDA::P00366 (558 letters) >FitnessBrowser__Pedo557:CA265_RS03475 Length = 473 Score = 445 bits (1145), Expect = e-129 Identities = 243/477 (50%), Positives = 316/477 (66%), Gaps = 15/477 (3%) Query: 82 EDKLVEDL-KTRETEEQKRNRVRSILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHS 140 E+K D+ K ++ Q N +L IK CN V FPIRR +G +EVI+ +R +HS Sbjct: 7 ENKFFADVCKNFDSAAQFTNHPEGLLNQIKTCNSVYRFQFPIRRGNG-FEVIDAWRVEHS 65 Query: 141 QHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEK 200 H +P KGGIRYS V+ DEV ALA+LMTYKCA+V+VPFGGAK G+KIN K Y+ ELE Sbjct: 66 HHMSPTKGGIRYSEMVNEDEVMALAALMTYKCAIVNVPFGGAKGGIKINTKQYSVAELET 125 Query: 201 ITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPI 260 ITRR+T EL KK FIGPG+DVPAPD +GEREMSWIADTY T+ ++A CVTGKPI Sbjct: 126 ITRRYTTELIKKNFIGPGIDVPAPDYGSGEREMSWIADTY-MTMNPGQLDALGCVTGKPI 184 Query: 261 SQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYL 320 + GI GR ATGRGV + + + A M+ +G G GDK +VQG GNVG HS ++L Sbjct: 185 ALHGIRGRKEATGRGVAYAVRECVEVAEDMAKIGFKAGLGDKRVIVQGLGNVGYHSAKFL 244 Query: 321 HRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGFPKAKIYEGSI--LEVDCDI 378 FGA + + E +G+I+NP+G++ E+ + G+ILGFP AK ++ S+ LE DCDI Sbjct: 245 AEFGATIVGLCEFEGAIYNPNGLNVDEVFAHRKNTGSILGFPGAKDFKNSMEGLEQDCDI 304 Query: 379 LIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVS 438 ++PAA E Q T+ N +KAKIIAEGANGPTTPEA+ IF E ++IPD+Y NAGGVTVS Sbjct: 305 IVPAALENQFTELNIRNIKAKIIAEGANGPTTPEAETIFTEMGGIIIPDMYCNAGGVTVS 364 Query: 439 YFEWLNNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRIS 498 YFEWL NL+HV++GR+ +Y +SN +L+ +LE GK I+P + Sbjct: 365 YFEWLKNLSHVAFGRMENRYAANSNANLI----NTLENLTGK-----TILPEHRLM-IVK 414 Query: 499 GASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGV 555 GASE ++V+SGL TM S +I T M LRTAA+VN+I+K+ Y GV Sbjct: 415 GASEMELVNSGLEDTMIHSYHEIRETLMNKPATQTLRTAAFVNSIDKIAVSYMNLGV 471 Lambda K H 0.318 0.136 0.404 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: 671 Number of extensions: 21 Number of successful extensions: 5 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: 558 Length of database: 473 Length adjustment: 35 Effective length of query: 523 Effective length of database: 438 Effective search space: 229074 Effective search space used: 229074 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: 52 (24.6 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