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 WP_028584142.1 G494_RS0108195 aminomethyl-transferring glycine dehydrogenase
Query= curated2:Q6ARJ7 (450 letters) >NCBI__GCF_000429965.1:WP_028584142.1 Length = 445 Score = 582 bits (1499), Expect = e-170 Identities = 283/444 (63%), Positives = 348/444 (78%), Gaps = 1/444 (0%) Query: 1 MRYLPHTEEEIQEMLEVVGKESLDDLFSSVPAECRYQGDIP-IPAALTEWQLKDHFAALM 59 MRYLPHT+EEI ML+V G SL+DLF+++P CR +P AL+EW+L H AL Sbjct: 1 MRYLPHTQEEISAMLQVTGNSSLEDLFATIPDTCRMSDQWEQLPEALSEWELDSHIQALA 60 Query: 60 SKNRVNQEHKVLIGAGSYDHYVPEILPSLMSRSEFLTAYTPYQPEVAQGTLQGIFEYQTL 119 V+Q VLIGAGSY H++P + +LMSRSEFLTAYTPYQPE+AQGTLQGIFEYQTL Sbjct: 61 DTMEVDQRATVLIGAGSYHHHIPATVKALMSRSEFLTAYTPYQPEMAQGTLQGIFEYQTL 120 Query: 120 TARLLGTDAVNASMYDGASALAESALMSFRIARKKKTVALSAAIHPHYREVVATYLQATD 179 +ARLLG D VNASMYDGASALAE+ LM R+A+KK+ VA+S A+HPHYREVV YL+ T Sbjct: 121 SARLLGMDVVNASMYDGASALAEAMLMGLRVAKKKRRVAISQAVHPHYREVVRAYLRPTP 180 Query: 180 FTIIELPVDAEGRTDLSSLAGIEGLASVAIQSPNFFGVVEDLQGCGEKIHDVDALFISCF 239 + ++ELP +GRTDLSSLA IE LA+VAIQSPNFFGV+EDL GE+IH ALFI+ F Sbjct: 181 YELVELPHGTDGRTDLSSLAEIEDLAAVAIQSPNFFGVIEDLGTAGEEIHGQGALFITAF 240 Query: 240 SEALAYGLLKSPGECGADIICGEGQSFGLGRSYGGPGVGMMGCRDKLVRNMPGRIVGQTL 299 SE LAYGLLK+PG CGADI+CGEGQSFGL RS+GGPG+GM GCR RN+PGR+VG+T Sbjct: 241 SEPLAYGLLKNPGACGADIVCGEGQSFGLSRSFGGPGLGMFGCRQPFTRNLPGRLVGETR 300 Query: 300 DTKGKRGFVLTLATREQHIRREKATSNICSNQGICAMTAGMYMATLGGTGIRQLARLNYD 359 D GKRG+VLTLATREQHIRR+KATSNICSNQGICAMTAGMYMA+LGGTG+++LARLNYD Sbjct: 301 DLDGKRGYVLTLATREQHIRRDKATSNICSNQGICAMTAGMYMASLGGTGLQELARLNYD 360 Query: 360 KAAYLRSELIKLGAKPLFDAPVFNEFALRFPFDFERVREALKEESVVAGLSLEAYYPDLQ 419 K+ YL + L + GA+ F AP FNEF + FP +F+ + L +++VAG+ L +YP++ Sbjct: 361 KSHYLMAALQERGARCCFSAPFFNEFVVEFPTEFKAAHQRLLAKNIVAGIDLGRWYPEMS 420 Query: 420 GAYLFCATETLKKEDIDRIVSSIK 443 G YLF TET+ +E +D I + ++ Sbjct: 421 GRYLFGVTETVSREVMDTIANEVQ 444 Lambda K H 0.320 0.136 0.393 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: 15 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: 450 Length of database: 445 Length adjustment: 33 Effective length of query: 417 Effective length of database: 412 Effective search space: 171804 Effective search space used: 171804 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 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