Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate GFF860 PGA1_c08740 glutamate dehydrogenase GluD
Query= BRENDA::P00366 (558 letters) >FitnessBrowser__Phaeo:GFF860 Length = 476 Score = 370 bits (951), Expect = e-107 Identities = 214/498 (42%), Positives = 304/498 (61%), Gaps = 32/498 (6%) Query: 63 DPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRSILRIIKPCNHVLSLSFPI 122 +P+F + V+ F+R S+++ L L+ + I+ CN ++ F + Sbjct: 6 EPSFRQSVDLMFNRAVSLMD--LPPGLEEK----------------IRVCNATYTVRFGV 47 Query: 123 RRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGA 182 R G + GYR+ HS+H P KGGIRY+ V+ DEV+ALA+LMTYKCA+V+ PFGG+ Sbjct: 48 RLRGGI-QTFTGYRSVHSEHMEPVKGGIRYAMGVNQDEVEALAALMTYKCALVEAPFGGS 106 Query: 183 KAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYAS 242 K G+ I+P+ Y ++ELE ITRRF ELAK+ I P +VPAPDM TGEREM+WIAD YA Sbjct: 107 KGGLCIDPRQYEEHELELITRRFAYELAKRDLINPSQNVPAPDMGTGEREMAWIADQYA- 165 Query: 243 TIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDK 302 + DINA ACVTGKP++ GGI GR+ ATGRGV + + F ++ M K Sbjct: 166 RMNTTDINAKACVTGKPLNAGGIAGRVEATGRGVQYALREFFRNPEDVAAANMDGKLDGK 225 Query: 303 TFVVQGFGNVGLHSMRYL-HRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGF 361 +VQG GNVG H+ ++L GAK V E DG + + +G+D + + + +G + G+ Sbjct: 226 RVIVQGLGNVGYHAAKFLMSEDGAKITAVIERDGGLIDENGLDIEAVFQWIANNGGVTGY 285 Query: 362 PKAKIYEGS--ILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLE 419 P A+ E +LE DCDILIPAA E + +NA +KA++I E ANGP T AD+I + Sbjct: 286 PDARYVENGALLLEEDCDILIPAALEGVINLTNAANIKARLIIEAANGPVTAGADEILRD 345 Query: 420 RNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFG 479 + ++IPD+Y NAGGVTVSYFEW+ NL+H+ +GR+ + E ++ + L++ E+L G Sbjct: 346 KGTVIIPDMYANAGGVTVSYFEWVKNLSHIRFGRMQRRQE-EARHQLVVDELEALSESLG 404 Query: 480 KHGGTIPIVPTAEFQDR-ISGASEKDIVHSGLAYTMERSARQIMRTAMK-YNLGLDLRTA 537 K P +F +R + GA E ++V SGL TM R+A Q MR N DLRTA Sbjct: 405 KTWTLNP-----KFTERYLRGADELELVRSGLDDTM-RTAYQSMREVWHGRNDVTDLRTA 458 Query: 538 AYVNAIEKVFRVYNEAGV 555 AY+ +I+KV + Y G+ Sbjct: 459 AYLVSIDKVAKSYRAKGL 476 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: 659 Number of extensions: 23 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: 476 Length adjustment: 35 Effective length of query: 523 Effective length of database: 441 Effective search space: 230643 Effective search space used: 230643 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