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 Ac3H11_1553 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P2 protein) (EC 1.4.4.2)
Query= curated2:Q9K936 (488 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1553 Length = 486 Score = 445 bits (1145), Expect = e-129 Identities = 237/469 (50%), Positives = 305/469 (65%), Gaps = 14/469 (2%) Query: 9 IFELSKPGRVGHSLPELDVLEQPVETLIPAEFLREEAPELPEVSELQLMRHYTALSKRNH 68 I +L +PG ++ P +P+ + LPEVSE+ ++RH+T LS+ +H Sbjct: 23 IIDLHRPGAASDVFAGRVLVSPP----LPSFARQRTVIGLPEVSEVDVVRHFTRLSQESH 78 Query: 69 GVDSGFYPLGSCTMKYNPKINEDVARYPGFANIHPYQPEAQVQGALRLMYELQTALAEIT 128 GVD+G YPLGSCTMKYNPK N+++AR PGF + HP Q ++G L LQ+ + E+T Sbjct: 79 GVDNGPYPLGSCTMKYNPKRNDELARLPGFVSAHPMQDVDTLRGVWELYERLQSMVNEVT 138 Query: 129 GMDEVTLQPAAGAQGEWTGLMLIRAYHEANGDTNRTKVIVPDSAHGTNPASATVAGFESV 188 GMD L PAAGA GE GL++IR Y G R V+VPDSAHGTNPASA +AGF+ Sbjct: 139 GMDACCLAPAAGAHGELAGLLVIRKYFAQLG-VIRPVVLVPDSAHGTNPASAAMAGFDCR 197 Query: 189 TVRTDEDGLVDLDHLREVVGEDTAALMLTNPNTLGLFEAHIVEMAAIIHEAGGKLYYDGA 248 V +D G VD+ LRE++ D AA MLTNP+TLGLFE IVE+A +H G LYYDGA Sbjct: 198 IVPSDLKGRVDMVSLREMLTPDVAAFMLTNPSTLGLFEDQIVEIADAVHANGSLLYYDGA 257 Query: 249 NSNAILGIARPGDMGFDVVHLNLHKTFTGPHGGGGPGSGPVGVKKELIPYLPKPVVVKDG 308 N NA++GI RPGDMGFDVVH+N+HKTF+ PHGGGGPG+GPV VK L YLP PVVV+ Sbjct: 258 NLNALMGIVRPGDMGFDVVHVNVHKTFSTPHGGGGPGAGPVAVKAGLAAYLPSPVVVRKD 317 Query: 309 DSYRLDYDRPHSIGRVKPYYGNFGINVRAYTYIRTMGPEGLRTVSEYAVLNANYMMRRLA 368 + D D P SIGR+K ++G+ G+ +RAY Y+RTMG GLR SE AVLNANY+ RLA Sbjct: 318 GVAQPDGDLPLSIGRMKSFHGHVGVLLRAYGYLRTMGARGLREASENAVLNANYLQHRLA 377 Query: 369 PYFDLPYDQHCKHEFVLSGRQQKKLGVRTLDIAKRLLDFGYHPPT------IYFPLNVEE 422 P Y Q CKHE +LSG +KL AKRL+D+G HPPT +YFP +++ Sbjct: 378 PMLPPVYRQFCKHETLLSG---EKLNTSARQFAKRLIDYGIHPPTLVGAGCVYFPGDLKS 434 Query: 423 CLMIEPTETESKETLDEFIEAMIQIAKEAEETPEVVQEAPHHTVIGRLD 471 ++IEPTETE+K +LD +E ++ E +V AP I R+D Sbjct: 435 AMLIEPTETETKASLDYQVEIFERVFNEDATDEALVGRAPLSRKIARID 483 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: 658 Number of extensions: 25 Number of successful extensions: 4 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: 486 Length adjustment: 34 Effective length of query: 454 Effective length of database: 452 Effective search space: 205208 Effective search space used: 205208 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