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 Ac3H11_1554 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P1 protein) (EC 1.4.4.2)
Query= curated2:Q24TH5 (446 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1554 Length = 457 Score = 355 bits (911), Expect = e-102 Identities = 190/438 (43%), Positives = 274/438 (62%), Gaps = 3/438 (0%) Query: 6 NTVDQQEQILTRIGVGSLEELFADIPESVRRQAQLKIREGLSELELVKYMGRLAAENKTV 65 +T + +L +G+ S+E+LFAD+P VR + +L + LSE EL++ + +A N TV Sbjct: 11 HTGSDVQSMLEVMGLDSVEQLFADVPAQVRLRRELDLPPALSEWELMRDVRSMADMNSTV 70 Query: 66 EEYTSYLGAGAYEHFIPSYVDQLLLRSEFYTAYTPYQPEISQGTLQAIYEFQTLVCELTG 125 +TS+LG GAYEH+IP+ VD ++ R EF TAYTPYQPE+SQG LQA++EFQ L+ L G Sbjct: 71 LSHTSFLGCGAYEHYIPAVVDAIVSRGEFLTAYTPYQPEMSQGLLQALFEFQVLLGRLLG 130 Query: 126 MDGANASMYDGASALAEAALMSCDATRRKKVLVPQTIHPEYREVLRTYLLPRGVEILEIP 185 + N S+YDGA+ALAE+ M C A+ +++V+V Q + +YREVL TYLLPRGV+++ + Sbjct: 131 RECVNCSVYDGATALAESCWMMCSASGKRRVVVAQAVWAQYREVLDTYLLPRGVQVVYVA 190 Query: 186 YQE--GAVDSEALEKALNT-EVAAVLIQSPNFFGMIEKAEEIGQMAHAKGGLLVMAVNPV 242 G VD+ A+ + + +VA V +QSPN G++E + + M G LL + VNP+ Sbjct: 191 QDPVTGMVDAAAMANLIASGDVAGVALQSPNALGLVEDVQAVALMCSQHGALLTVCVNPL 250 Query: 243 SLGLLKSPGELGADIVVGEGQPFGNPLNFGGPYLGFLACREKYVRRMPGRIVGATKDKNG 302 G L++PG LGADIVV EGQP G PL+ GGPY+G +AC + R +PGR+VG D NG Sbjct: 251 LCGWLEAPGALGADIVVCEGQPLGLPLSAGGPYVGIIACAKPLERYLPGRLVGRVHDLNG 310 Query: 303 KKGYVLTLQAREQHIRREKAASNICSNEALCALAFTIHLSGLGKRGLKEMARLNLQKAHY 362 + GY L + REQH+ R+KA S+ICSN+AL A+ IHL+ LG+R +A++N A Sbjct: 311 QLGYALVKEDREQHVARDKATSHICSNQALNAIRVAIHLACLGERNFMRIAQMNAANAAR 370 Query: 363 GAEEIGKLPGMSLAFQGPFFHEFVIKTEVSPRKINEALLSHKIIGGLELSRFYPELDQHL 422 E + + G+S G F+EF + V + + I G+ L + L Sbjct: 371 LRELLTSIDGVSALRSGVHFNEFAVALPVDVATFCTRMRNLGIFAGVPLEEGLVGHGRGL 430 Query: 423 LFCVTETKTKEDIDRLVA 440 L VTETK+ D++ VA Sbjct: 431 LVAVTETKSLADLEAYVA 448 Lambda K H 0.318 0.137 0.388 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: 508 Number of extensions: 19 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: 446 Length of database: 457 Length adjustment: 33 Effective length of query: 413 Effective length of database: 424 Effective search space: 175112 Effective search space used: 175112 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: 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