GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Pseudomonas fluorescens FW300-N2E3

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 AO353_07665 AO353_07665 serine hydroxymethyltransferase

Query= curated2:D3DKC4
         (427 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_07665
          Length = 417

 Score =  484 bits (1247), Expect = e-141
 Identities = 246/405 (60%), Positives = 302/405 (74%), Gaps = 2/405 (0%)

Query: 8   DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67
           D  +  A+  E  RQ  H+ELIASEN+TS  VMEAQGS +TNKYAEG P KRYYGGCE V
Sbjct: 12  DDALLAAMNAEELRQEDHIELIASENYTSKRVMEAQGSGLTNKYAEGYPGKRYYGGCEHV 71

Query: 68  DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127
           D  E LAIERAK LF A++ANVQPHSG+ AN AVY+A+L+ GDTI+GM L+HGGHLTHGA
Sbjct: 72  DKVEALAIERAKLLFGADYANVQPHSGSSANSAVYLALLQAGDTILGMSLAHGGHLTHGA 131

Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187
           KV+ SGK+YNAV YG+  +T LIDYD++ RLA E KPK+IV G SAY + +D+ + R+IA
Sbjct: 132 KVSSSGKLYNAVQYGIDTKTGLIDYDEVERLAVECKPKMIVAGFSAYSKTLDFPRFRQIA 191

Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK--KEFAKD 245
           D VGA L VDMAH AGL+A G+YPNP+PYA  VT+TTHKTLRGPR G IL K  +E  K 
Sbjct: 192 DKVGALLFVDMAHVAGLVAAGLYPNPLPYADVVTTTTHKTLRGPRGGLILAKANEEIEKK 251

Query: 246 IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS 305
           ++ +VFPG QGGPLMHVIA KAV FKEA+   FK Y +QV+ NA+ +A  FIK G+ VVS
Sbjct: 252 LNAAVFPGAQGGPLMHVIAGKAVCFKEALEPGFKAYQQQVIDNAQAMASVFIKRGYDVVS 311

Query: 306 GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTT 365
           GGTD+H+ L+ L   GLTG+E + ALG+A+ITVNKNAVP DP  P  TSG+R+GTPA+TT
Sbjct: 312 GGTDNHLFLVSLIRQGLTGKEADAALGRAHITVNKNAVPNDPQSPFVTSGLRIGTPAVTT 371

Query: 366 RGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410
           RG K  Q   +A  I  ++ N+GD  V   V + V  +C  FP+Y
Sbjct: 372 RGFKVTQCIELAGWICDILDNLGDADVEANVAKHVAAVCADFPVY 416


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: 26
Number of successful extensions: 2
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: 417
Length adjustment: 32
Effective length of query: 395
Effective length of database: 385
Effective search space:   152075
Effective search space used:   152075
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