GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Magnetospirillum magneticum AMB-1

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_011384736.1 AMB_RS11815 serine hydroxymethyltransferase

Query= curated2:D3DKC4
         (427 letters)



>NCBI__GCF_000009985.1:WP_011384736.1
          Length = 427

 Score =  482 bits (1241), Expect = e-141
 Identities = 243/413 (58%), Positives = 300/413 (72%), Gaps = 6/413 (1%)

Query: 4   LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63
           L   D E++ AI +E +RQ   +ELIASEN  S AV+EAQGSVMTNKYAEG P KRYYGG
Sbjct: 14  LSERDPEVFAAITQELKRQQDQIELIASENIVSRAVLEAQGSVMTNKYAEGYPGKRYYGG 73

Query: 64  CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123
           CEFVDIAE LAI RA  +F   +ANVQP SG+QAN  V+MA+L+PGDTIMGM L+ GGHL
Sbjct: 74  CEFVDIAESLAISRACQIFGCSYANVQPSSGSQANQGVFMALLQPGDTIMGMSLAAGGHL 133

Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183
           THGA  N SGK + AV YGV  +   ID+ ++  LA+ H+PKLI+ G SAYPR ID+A+ 
Sbjct: 134 THGAAPNQSGKWFKAVQYGVRQQDSQIDFAEVEELARTHRPKLIIAGGSAYPRTIDFARF 193

Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK-KEF 242
           R+IAD VGA+ MVDMAH+AGL+AGGVYPNP+P+AH VT+TTHKTLRGPR G IL    + 
Sbjct: 194 RKIADEVGAFFMVDMAHFAGLVAGGVYPNPLPHAHVVTTTTHKTLRGPRGGMILSNDADI 253

Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302
            K I+ ++FPGIQGGPLMHVIA KAVAF EA+  EFK YA+QVV NAR LA+  ++ G  
Sbjct: 254 GKKINSAIFPGIQGGPLMHVIAGKAVAFGEALKPEFKLYAKQVVDNARALADTLVRRGLD 313

Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362
           +VSGGTDSH++L+DLR   LTG+  E +L  A +T NKN +PFDP  P  TSG+RLGTPA
Sbjct: 314 IVSGGTDSHLMLVDLRPKKLTGKAAEASLEHAGMTCNKNGIPFDPEKPTITSGVRLGTPA 373

Query: 363 MTTRGMKEDQMRIIARLISKVIKNIG----DEKVIE-YVRQEVIEMCEQFPLY 410
            TTRG   ++ + +  LI  V+  +     D    E   R EV E+C +FP+Y
Sbjct: 374 ATTRGFGVEEFKKVGELIGDVLDGLAANPEDNSAAEARARAEVAELCRRFPIY 426


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: 577
Number of extensions: 24
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: 427
Length adjustment: 32
Effective length of query: 395
Effective length of database: 395
Effective search space:   156025
Effective search space used:   156025
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.

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