Align Probable glycine dehydrogenase (decarboxylating) subunit 2; EC 1.4.4.2; Glycine cleavage system P-protein subunit 2; Glycine decarboxylase subunit 2; Glycine dehydrogenase (aminomethyl-transferring) subunit 2 (uncharacterized)
to candidate 206868 DVU1424 glycine cleavage system P protein, subunit 2
Query= curated2:Q9K936 (488 letters) >MicrobesOnline__882:206868 Length = 481 Score = 510 bits (1313), Expect = e-149 Identities = 264/479 (55%), Positives = 327/479 (68%), Gaps = 11/479 (2%) Query: 9 IFELSKPGRVGHSLPELDVLEQPVETLIPAEFLREEAPELPEVSELQLMRHYTALSKRNH 68 +F S PGR +LP + ++PA LR +AP LPEVSEL ++RH+T LS+ N+ Sbjct: 4 VFAKSVPGRSA-ALPSAP--SRKAADMLPAGLLRSKAPRLPEVSELDVVRHFTGLSRLNY 60 Query: 69 GVDSGFYPLGSCTMKYNPKINEDVARYPGFANIHPYQPEAQ-----VQGALRLMYELQTA 123 VD FYPLGSCTMKYNPK E VA PGF +HP + + QGAL +M+E + Sbjct: 61 SVDGNFYPLGSCTMKYNPKFTEHVAALPGFTRLHPLMAQLKGAGQYTQGALEVMWETERL 120 Query: 124 LAEITGMDEVTLQPAAGAQGEWTGLMLIRAYHEANGDTNRTKVIVPDSAHGTNPASATVA 183 L EI GM TL P AGA GE TG+MLI AYH+ G+ +TK+I PDSAHGTNPASA +A Sbjct: 121 LCEINGMAAFTLHPMAGAHGELTGVMLIAAYHKDKGN-RKTKIICPDSAHGTNPASAALA 179 Query: 184 GFESVTVRTDEDGLVDLDHLREVVGEDTAALMLTNPNTLGLFEAHIVEMAAIIHEAGGKL 243 G+E V + + +DGLVD D L V+ ++ AALM+T PNTLGLFE H+ + + L Sbjct: 180 GYEVVNIES-KDGLVDPDALEAVLDDEVAALMMTCPNTLGLFEKHLPRIVEKLRAVDALL 238 Query: 244 YYDGANSNAILGIARPGDMGFDVVHLNLHKTFTGPHGGGGPGSGPVGVKKELIPYLPKPV 303 YYDGAN NAI+G R GD+GFDVVHLNLHKTF PHGGGGPGSGPVGV L PYLP Sbjct: 239 YYDGANLNAIMGKMRVGDVGFDVVHLNLHKTFGTPHGGGGPGSGPVGVSARLEPYLPISR 298 Query: 304 VVKDGDS-YRLDYDRPHSIGRVKPYYGNFGINVRAYTYIRTMGPEGLRTVSEYAVLNANY 362 V K+ D + L+YD P SIG V P+YGNFG+ ++AY YI +G EGL SE+AVLNANY Sbjct: 299 VEKERDGHFFLNYDYPKSIGYVAPFYGNFGVLLKAYAYILRLGAEGLTRASEFAVLNANY 358 Query: 363 MMRRLAPYFDLPYDQHCKHEFVLSGRQQKKLGVRTLDIAKRLLDFGYHPPTIYFPLNVEE 422 M +L D+P+D+ C HEFV S + GVR LDIAK LLD GYH PTIYFPL V+E Sbjct: 359 MRCKLRGVLDIPHDRTCMHEFVASACNTAECGVRALDIAKALLDKGYHAPTIYFPLIVKE 418 Query: 423 CLMIEPTETESKETLDEFIEAMIQIAKEAEETPEVVQEAPHHTVIGRLDETTAARKPIL 481 CLM EPTETES+ETLD F++ + I ++ +TP+ + +AP HT + RLDET AAR +L Sbjct: 419 CLMFEPTETESRETLDAFMDDLASIVEQGRQTPDALHDAPLHTPVRRLDETAAARNMVL 477 Lambda K H 0.317 0.137 0.403 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: 639 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: 488 Length of database: 481 Length adjustment: 34 Effective length of query: 454 Effective length of database: 447 Effective search space: 202938 Effective search space used: 202938 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: 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