Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1; L-threonine/L-allo-threonine aldolase; EC 4.1.2.48 (uncharacterized)
to candidate GFF1172 PGA1_c11870 serine hydroxymethyltransferase GlyA
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__Phaeo:GFF1172 Length = 432 Score = 501 bits (1289), Expect = e-146 Identities = 251/415 (60%), Positives = 316/415 (76%), Gaps = 7/415 (1%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L D E++ +I E RQ +ELIASEN S AVMEAQG+V+TNKYAEG P +RYYGG Sbjct: 16 LAERDPELFGSITDELGRQRDEIELIASENIVSAAVMEAQGTVLTNKYAEGYPGRRYYGG 75 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 C++VD+AE+LAI+RAK LFD E ANVQP+SG+QAN V+ A++KPGDTI+GMDL+ GGHL Sbjct: 76 CQYVDVAENLAIDRAKKLFDCEFANVQPNSGSQANQGVFQALIKPGDTILGMDLASGGHL 135 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THGA+ N SGK +NAV+YGV E LIDYDQ+ LA EH+PKLI+ G SA PRVID+A+ Sbjct: 136 THGARPNQSGKWFNAVHYGVREEDCLIDYDQIEALAVEHQPKLIIAGGSAIPRVIDFARF 195 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK-KEF 242 REIAD VGAYL VDMAH+AGL+A G +P+P P+AH T+TTHKTLRGPR G IL + Sbjct: 196 REIADKVGAYLHVDMAHFAGLVAAGEHPSPFPHAHVATTTTHKTLRGPRGGMILTNDADI 255 Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302 AK ++ ++FPGIQGGPLMHVIAAKAVAF EA+ EFK+Y +QV ANA L+++ IK G Sbjct: 256 AKKVNSAIFPGIQGGPLMHVIAAKAVAFGEALRPEFKDYQKQVRANAVALSDQLIKGGLD 315 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +V+GGTD+H++L+DLR G+TG V++ALG+A+IT NKN +PFDP P TSGIRLGTPA Sbjct: 316 IVTGGTDTHVMLVDLRPKGVTGNIVDKALGRAHITTNKNGIPFDPEKPTVTSGIRLGTPA 375 Query: 363 MTTRGMKEDQMRIIARLISKVIKNI------GDEKVIEYVRQEVIEMCEQFPLYP 411 TTRG E + R IA LI +V+ + G+ V VR++V +C +FPLYP Sbjct: 376 GTTRGFGEAEFREIADLIIEVVDGLAANGEDGNATVEASVREKVAALCARFPLYP 430 Lambda K H 0.319 0.136 0.395 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: 613 Number of extensions: 22 Number of successful extensions: 3 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: 427 Length of database: 432 Length adjustment: 32 Effective length of query: 395 Effective length of database: 400 Effective search space: 158000 Effective search space used: 158000 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