GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Pseudomonas fluorescens FW300-N2C3

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 AO356_16850 AO356_16850 serine hydroxymethyltransferase

Query= curated2:D3DKC4
         (427 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16850
          Length = 412

 Score =  493 bits (1270), Expect = e-144
 Identities = 240/407 (58%), Positives = 307/407 (75%)

Query: 4   LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63
           L N D  I   I +E  RQ  HLELIASEN+ S  V++AQGSV+TNKYAEG P KRYYGG
Sbjct: 3   LQNFDPAIARLIDRERNRQETHLELIASENYVSEEVLQAQGSVLTNKYAEGYPGKRYYGG 62

Query: 64  CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123
           C+ VD  E+LAIERA+ LF+ E+ NVQPHSG+QAN AV++AVL+PGDTI+GM L+HGGHL
Sbjct: 63  CKVVDEIENLAIERARKLFNCEYVNVQPHSGSQANQAVFLAVLEPGDTILGMSLAHGGHL 122

Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183
           THGA VNFSGK+Y A  YG+  ET  +DY+++  LA+EH+PK+I+ GASAY R +D+ + 
Sbjct: 123 THGASVNFSGKLYRAFSYGLDTETETLDYEEMEALAREHRPKMIIAGASAYSRTLDFQRF 182

Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243
           R+I D VGAYLMVDMAHYAGLIA GVYP+PV  A F+TSTTHKTLRGPR G IL K ++A
Sbjct: 183 RKICDEVGAYLMVDMAHYAGLIAAGVYPSPVGIADFITSTTHKTLRGPRGGLILAKAQYA 242

Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKV 303
             +DK++FP  QGGPLMHVIAAKAVAF EA+   FK Y ++V+ NARV+A+   + G +V
Sbjct: 243 ALLDKTIFPVYQGGPLMHVIAAKAVAFNEALGDGFKHYQQRVIDNARVMADVLTRRGLRV 302

Query: 304 VSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAM 363
           VSGGTD H+ LLDLR   +TG++ E  L  A+IT+NKNA+P DP  P  TSGIR+GTPA+
Sbjct: 303 VSGGTDCHMFLLDLRSMNITGKDAEALLESAHITLNKNAIPNDPQKPAVTSGIRIGTPAL 362

Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410
           TTRG  E +   +A LI+ +++   +   ++  R+ V+ +CE FP+Y
Sbjct: 363 TTRGFGEAECAEVANLIADLLEQPDNAARLDNTRRRVMHLCECFPVY 409


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: 575
Number of extensions: 28
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: 427
Length of database: 412
Length adjustment: 32
Effective length of query: 395
Effective length of database: 380
Effective search space:   150100
Effective search space used:   150100
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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