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 AZOBR_RS10460 AZOBR_RS10460 glycine dehydrogenase
Query= curated2:Q2RPV1 (448 letters) >FitnessBrowser__azobra:AZOBR_RS10460 Length = 446 Score = 574 bits (1479), Expect = e-168 Identities = 294/448 (65%), Positives = 347/448 (77%), Gaps = 2/448 (0%) Query: 1 MRYLPHSEADRAAMLATIGAASVEDLFRDVPREALDQAAFDALPDHGGEMEVERALSALA 60 MRYLP +EADR +ML IG SV++LFRDVP A + L +H GE+EV+RALSA+A Sbjct: 1 MRYLPLTEADRRSMLEAIGVPSVDELFRDVPEAARLSGPIEGLSNHMGELEVDRALSAMA 60 Query: 61 ARNLTAGSVPCFLGAGSYRHHVPAAVDALIQRGEFLTSYTPYQAEVSQGTLQYLFEFQTQ 120 +NL AGSVP FLGAG+YRHH+PA VD L+QRGEFLT+YTPYQ EVSQGTLQ LFEFQTQ Sbjct: 61 GKNLPAGSVPSFLGAGAYRHHIPATVDHLVQRGEFLTAYTPYQPEVSQGTLQVLFEFQTQ 120 Query: 121 VALITGMEVANASMYDGATACAEAAAMAVRITRRRKVLMAGGLHPHYTATTQTLLACLGH 180 V+L+TGM+VANASMYDGATACAEA MA R+TRR+K +++GGLHPHY TT T +G Sbjct: 121 VSLLTGMDVANASMYDGATACAEAVMMANRVTRRKKAVLSGGLHPHYRDTTTTDARFIGF 180 Query: 181 EGEGLPPDPLALGDLIGRVGSDTACVIVQNPDFFGRLRDLSPLAEACHAAGALLVVAVCE 240 E +PP P DL+ V DT+CV+VQNPD FG +RD + L +AC A GALL+V V E Sbjct: 181 ETVVMPPAPTGGEDLLAAVDGDTSCVVVQNPDVFGHVRDYTELGKACQAKGALLIVVVTE 240 Query: 241 PVSLGLVAPPGAMGADIVVAEGHALGSPTGFGGPGVGLFATREKYLRQMPGRLAGETLDE 300 VSLGL+ PPG MGADIV AEG +LG+ FGGP VGLFA +EK +RQMPGRL G+T+D Sbjct: 241 AVSLGLLTPPGDMGADIVAAEGQSLGNALNFGGPYVGLFAVKEKLVRQMPGRLCGQTVDA 300 Query: 301 SGKRGYVLTLSTREQHIRREKATSNICTNSGLIALAFTIHMTLLGEAGFTRLAWINHANA 360 G+RG+VLTLSTREQHIRREKATSNICTNSGL ALAF+IH++LLGE GFTRLA INHA A Sbjct: 301 DGRRGFVLTLSTREQHIRREKATSNICTNSGLCALAFSIHLSLLGEEGFTRLAEINHAKA 360 Query: 361 VALAEKLARVKGVKVLPETFFNEFTLRLPKPAAEVVEALAARSILAGVPVSRFLPTYPEL 420 V LA+KLA V GV+++ ++FFNEFT++LPKPAAEVVEALA R IL GVP SR L Sbjct: 361 VQLADKLAAVTGVEIVNDSFFNEFTVKLPKPAAEVVEALAQRGILGGVPASRLFG--GGL 418 Query: 421 ANLLLVNATELTTPEDADALVAALKEVL 448 +LL+V ATE T D DA AL EVL Sbjct: 419 DDLLIVAATETNTESDMDAFATALAEVL 446 Lambda K H 0.320 0.135 0.392 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: 516 Number of extensions: 18 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: 448 Length of database: 446 Length adjustment: 33 Effective length of query: 415 Effective length of database: 413 Effective search space: 171395 Effective search space used: 171395 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