GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1451 Serine hydroxymethyltransferase (EC 2.1.2.1)

Query= curated2:D3DKC4
         (427 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1451
          Length = 417

 Score =  493 bits (1268), Expect = e-144
 Identities = 243/405 (60%), Positives = 313/405 (77%), Gaps = 3/405 (0%)

Query: 8   DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67
           DA+++ A+ +E +RQ  H+ELIASEN+TS AVMEAQGSV+TNKYAEG P KRYYGGCE+V
Sbjct: 12  DADLFAAMEQEAQRQEEHIELIASENYTSPAVMEAQGSVLTNKYAEGYPGKRYYGGCEYV 71

Query: 68  DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127
           DI E LAI+RAK LF A++ANVQPH+G+QAN AVY+A+L  GDTI+GM L+HGGHLTHGA
Sbjct: 72  DIVEQLAIDRAKELFGADYANVQPHAGSQANSAVYLALLSAGDTILGMSLAHGGHLTHGA 131

Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187
            V+ SGK+YNA+ YG+     LIDYD++ RLA EHKPK+IV G SAY +++D+ + R IA
Sbjct: 132 SVSSSGKLYNAIQYGI-DANGLIDYDEVERLAVEHKPKMIVAGFSAYSQILDFPRFRAIA 190

Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK--KEFAKD 245
           D VGAYL VDMAH AGL+A GVYPNPVP+A  VT+TTHKTLRGPR G IL +   +  K 
Sbjct: 191 DKVGAYLFVDMAHVAGLVAAGVYPNPVPFADVVTTTTHKTLRGPRGGLILARANADIEKK 250

Query: 246 IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS 305
           ++ +VFPG QGGPL HVIAAKA+ FKEA+  EFK Y +QVV NA+ +A  FI+ GF VVS
Sbjct: 251 LNSAVFPGAQGGPLEHVIAAKAICFKEALQPEFKAYQQQVVKNAQAMAGVFIERGFDVVS 310

Query: 306 GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTT 365
           GGT +H+ LL L    ++G++ + ALGKA ITVNKN+VP DP  P  TSG+R GTPA+TT
Sbjct: 311 GGTQNHLFLLSLIKQEISGKDADAALGKAFITVNKNSVPNDPRSPFVTSGLRFGTPAVTT 370

Query: 366 RGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410
           RG KE + + +A  I  ++ ++ +E VI+ VR++V  +C++ P+Y
Sbjct: 371 RGFKEAECKELAGWICDILADLNNEAVIDAVREKVKAICKKLPVY 415


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: 599
Number of extensions: 30
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: 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