GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Sphingobium czechense LL01

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 WP_066603023.1 V473_RS09495 serine hydroxymethyltransferase

Query= curated2:D3DKC4
         (427 letters)



>NCBI__GCF_001046645.1:WP_066603023.1
          Length = 433

 Score =  486 bits (1250), Expect = e-142
 Identities = 240/414 (57%), Positives = 311/414 (75%), Gaps = 7/414 (1%)

Query: 4   LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63
           L + D EI+ A   E +RQ   +ELIASEN  S AV+EA GS+ TNKYAEG P KRYYGG
Sbjct: 20  LASADPEIFGACRNELKRQQDKIELIASENIVSKAVLEAAGSIFTNKYAEGYPGKRYYGG 79

Query: 64  CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123
           CE+ D+ E LAIERAK LF A  ANVQP+SG+Q N AV++A+L+PGDT MG+DLS GGHL
Sbjct: 80  CEYADVVETLAIERAKELFGANFANVQPNSGSQMNQAVFLALLQPGDTFMGLDLSSGGHL 139

Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183
           THG+ VN SGK +  V YGV  + HLID D++ R+A+E KPKLI+ G +AY RV D+ + 
Sbjct: 140 THGSPVNMSGKWFKPVAYGVRADDHLIDMDEVARIARECKPKLIICGGTAYSRVWDFKRF 199

Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKE-F 242
           REIAD VGAYL+ DM+H++GL+AGG +P+PVPYAH  T+TTHK+LRGPRSG +L   E  
Sbjct: 200 REIADEVGAYLLADMSHFSGLVAGGAHPSPVPYAHVTTTTTHKSLRGPRSGIVLTNDEAI 259

Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302
           AK I+ ++FPG+QGGPLMH+IAAKAVAFKEA++ EFK YA Q+VANAR L+E     G  
Sbjct: 260 AKKINSAIFPGMQGGPLMHIIAAKAVAFKEALTPEFKAYAHQIVANARALSETLADAGLS 319

Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362
           +VSGGTD+H++L+DLR    TG+  E+AL +A IT NKN VPFD   P  TSG+RLGTPA
Sbjct: 320 IVSGGTDNHLMLVDLRAKNTTGKAAEKALDRAYITCNKNNVPFDTASPFVTSGVRLGTPA 379

Query: 363 MTTRGMKEDQMRIIARLISKVIKNI------GDEKVIEYVRQEVIEMCEQFPLY 410
            TTRG +E++ R I RLI++V++ +      GD +V ++VR++V+ +  +FP+Y
Sbjct: 380 GTTRGFREEEFREIGRLIAEVVEGLKRNGDEGDGQVEQHVREKVLGLTARFPIY 433


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: 593
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: 433
Length adjustment: 32
Effective length of query: 395
Effective length of database: 401
Effective search space:   158395
Effective search space used:   158395
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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