Align Probable glycine dehydrogenase (decarboxylating) subunit 1; EC 1.4.4.2; Glycine cleavage system P-protein subunit 1; Glycine decarboxylase subunit 1; Glycine dehydrogenase (aminomethyl-transferring) subunit 1 (uncharacterized)
to candidate Ga0059261_3258 Ga0059261_3258 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain
Query= curated2:Q2G781 (452 letters) >FitnessBrowser__Korea:Ga0059261_3258 Length = 452 Score = 671 bits (1731), Expect = 0.0 Identities = 334/452 (73%), Positives = 380/452 (84%) Query: 1 MRYLPLTDADRSAMLSVVGAGSVDELFADVPAEARLSAPIAGLPNHASEMAVERHMARLS 60 MRYLPLT DR AML+ VGA ++D+LF DVP ARLS PIAGLP HASE+AVERHMA L+ Sbjct: 1 MRYLPLTPNDRQAMLAAVGAAAIDDLFVDVPESARLSGPIAGLPPHASELAVERHMAALA 60 Query: 61 ANNVTAGSVPFFLGAGAYRHHVPATVDHMIQRGEFLTAYTPYQPEIAQGTLQVLFEFQTQ 120 N++AG PFFLG GAYRHHVPA+VDH+IQRGEFLTAYTPYQPEIAQGTLQV+FEFQTQ Sbjct: 61 RKNLSAGEAPFFLGCGAYRHHVPASVDHIIQRGEFLTAYTPYQPEIAQGTLQVMFEFQTQ 120 Query: 121 VARLFGTDVANASLYDGSTACWEAIAMAGRITKRGKALLSGGLHPHYVETARTMARFTGD 180 VARL GTDVANAS+YDGSTACWEAI MA RITKRGKA+LSGGLHPHYV A TMA++TGD Sbjct: 121 VARLLGTDVANASMYDGSTACWEAIGMARRITKRGKAILSGGLHPHYVSVANTMAKYTGD 180 Query: 181 VLDTSAPVLTAAPDDDALVARIDGETSCVVVQYPDILGRIPDLAKIAAAAQAQGALLITV 240 L T+ P LTA PD DAL+ ID ETSCVVVQYPDILGRI DL+ +AAA QA+ ALL+ V Sbjct: 181 TLVTAIPELTAEPDTDALIGMIDDETSCVVVQYPDILGRISDLSDLAAACQAKKALLVAV 240 Query: 241 VTEPVALGVLQSPGSLGADIVVGEGQSLGVGLQFGGPYLGLFGCREKYLRQIPGRLCGET 300 VTEPVALG ++SPG +GADIVVGEGQS+GVGLQFGGPY+GLFGC+EKY+RQ+PGRL GET Sbjct: 241 VTEPVALGAIRSPGEMGADIVVGEGQSIGVGLQFGGPYVGLFGCKEKYVRQMPGRLTGET 300 Query: 301 VDADGKRGFVLTLSTREQHIRREKATSNICTNSGLCALAFSIHLTLLGGSGLADMARLSH 360 VDA+GKRGFVLTLSTREQHIRREKATSNICT+S LCALA+SIH+TLLG GL +A L+H Sbjct: 301 VDAEGKRGFVLTLSTREQHIRREKATSNICTSSVLCALAWSIHMTLLGEKGLRQLAALNH 360 Query: 361 LAARKTAAALAQVSGIEVVNSHFFNEFTVALPHDARQIVRDLADRHVLGGVSLGRLYPQE 420 A A LA+V G+E+V FFNEFT+ L +AR IVR+LAD+ +L GVSLGRLYP E Sbjct: 361 AGASAAADRLAKVPGVELVTPVFFNEFTLKLSKEARPIVRELADKGILAGVSLGRLYPGE 420 Query: 421 AALANGMVVAATECTTDEDIAALVAALKEVLA 452 AL NG+VVA TE TT ED+ L AAL+E LA Sbjct: 421 GALENGLVVAVTETTTAEDVETLAAALEEALA 452 Lambda K H 0.320 0.135 0.389 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: 632 Number of extensions: 21 Number of successful extensions: 1 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: 452 Length of database: 452 Length adjustment: 33 Effective length of query: 419 Effective length of database: 419 Effective search space: 175561 Effective search space used: 175561 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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