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 8499452 DvMF_0224 glycine dehydrogenase subunit 1 (RefSeq)
Query= curated2:Q311A7 (443 letters) >FitnessBrowser__Miya:8499452 Length = 443 Score = 692 bits (1787), Expect = 0.0 Identities = 336/443 (75%), Positives = 391/443 (88%) Query: 1 MPYTPHTPEEIRQMLDVIGVKSIDDLFAEIPPEMQPRSFDIPEGMSEMEVCARIQRMAAK 60 MP+ PH+PEE+R+ML VIGV+SI+DLF +IP EM+PRSF++P G+SEM+V A+++ MAA+ Sbjct: 1 MPFIPHSPEEVREMLSVIGVQSIEDLFVDIPAEMRPRSFELPLGLSEMQVLAKMEEMAAR 60 Query: 61 NRIDLVSYLGAGFYDHHIPKAVDNLVSRGEFYTAYTPYQPEASQGTLQAIFEYQTAVCRL 120 NR D+VS+LG GFY HHIP AVD LVSRGEFYTAYTPYQPEASQGTLQAIFEYQTAVCRL Sbjct: 61 NRTDVVSFLGGGFYSHHIPAAVDALVSRGEFYTAYTPYQPEASQGTLQAIFEYQTAVCRL 120 Query: 121 MEMEVANASVYDGGSAIFEAMMMAARATRRSKLVIDEALSPIYRTMLASYTSNLNMELVT 180 ++M+ ANASVYDGGSAIFEAMMMA RAT+R KLVIDEA+SPI+RTMLASYTSNL+++LVT Sbjct: 121 LDMDCANASVYDGGSAIFEAMMMAVRATKRRKLVIDEAVSPIWRTMLASYTSNLSLDLVT 180 Query: 181 VAHNEGRSDKQALMDAVDDKCAAVVVQNPNFFGAVDDFTELFTHARSCNALGVISVYPVM 240 V +GRSD A+ AVD CAAVVVQNPNFFG V+DFT+LF HA+S A VISVYPVM Sbjct: 181 VPQVDGRSDMAAMKAAVDTGCAAVVVQNPNFFGVVEDFTDLFAHAKSQKAASVISVYPVM 240 Query: 241 QSVLKTPGEMGADIAVADGQSLGMPLSFGGPYLGIMTCTKKLARQIPGRIAGRTKDVDGK 300 QSVLKTPGEMGADIAVA+GQSLG PLSFGGPYLGIMTCTK + RQ+PGRI GRT D +G+ Sbjct: 241 QSVLKTPGEMGADIAVAEGQSLGQPLSFGGPYLGIMTCTKDMVRQMPGRIVGRTNDTEGR 300 Query: 301 TGYVLTLQAREQHIRRAKATSNICSNQALCALRAIIHMCLTGPEGLVRTAELSMERAHYA 360 TGYVLTLQAREQHIRRAKATSNICSNQALCALR ++H+CL GPEGL+RTAELSMERA YA Sbjct: 301 TGYVLTLQAREQHIRRAKATSNICSNQALCALRTLVHLCLLGPEGLIRTAELSMERARYA 360 Query: 361 ADRLTALPGVSLLHDAPFCNEFALRLPVSAYDVVDRLVNHGVVPGFPLGGYYAGMDDVLL 420 +RLTA+ GV L+ APF NEFA+RLP+ A++ VDRL G VPGFP+G YYAGMDDVLL Sbjct: 361 MERLTAIAGVRPLNTAPFGNEFAVRLPIPAFEAVDRLTARGYVPGFPVGRYYAGMDDVLL 420 Query: 421 VACTEKHSFEQIGIMAELVGGML 443 VACTEK+SFEQ+GI+AE++GG+L Sbjct: 421 VACTEKNSFEQVGILAEMLGGIL 443 Lambda K H 0.321 0.136 0.398 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: 672 Number of extensions: 15 Number of successful extensions: 1 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: 443 Length of database: 443 Length adjustment: 32 Effective length of query: 411 Effective length of database: 411 Effective search space: 168921 Effective search space used: 168921 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 (21.9 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