GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Lactobacillus shenzhenensis LY-73

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_022528623.1 L248_RS03165 phosphate acetyltransferase

Query= metacyc::MONOMER-13062
         (328 letters)



>NCBI__GCF_000469325.1:WP_022528623.1
          Length = 328

 Score =  385 bits (989), Expect = e-112
 Identities = 199/326 (61%), Positives = 247/326 (75%), Gaps = 4/326 (1%)

Query: 1   MDLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALN 60
           MDLF SL+ KI+ + I++VFPEG + RII AA RL  + +  P+LLG  A ++  A+   
Sbjct: 1   MDLFASLQQKIQGKDIRIVFPEGTEPRIIGAAVRLNAERILTPILLGTPAAVQAAAEKAG 60

Query: 61  VSLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVD 120
            +L  I+I+D ++        +V + V+RRKGK T +Q    L+DPNYFGT +VY    D
Sbjct: 61  FTLGNIQILDPQDYADF--DSLVASFVDRRKGKNTKEQGETMLRDPNYFGTMLVYTGLAD 118

Query: 121 GMVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGD--QRYLFADCAININPNETQ 178
           GMVSGA H TG+TVRPALQIIKTKPGV+  SG+F+MQ+G   +RY+FADCAINI+PN  +
Sbjct: 119 GMVSGAVHSTGETVRPALQIIKTKPGVSRTSGAFIMQRGRDAERYIFADCAINIDPNAQE 178

Query: 179 LAEIAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEM 238
           LAEIAV S +TA+LFDIDP VA+LSFST GSAK+P+V+KV  ATK+A E+ P + +DGE+
Sbjct: 179 LAEIAVASAQTAKLFDIDPHVAMLSFSTKGSAKAPQVDKVVEATKIAHELAPDLDLDGEL 238

Query: 239 QFDAAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNK 298
           QFDAAFVP+V   K   S VAG ATVF+FP+LQSGNIGYKIAQR G FEAIGPILQGLNK
Sbjct: 239 QFDAAFVPSVGAQKAPGSTVAGKATVFIFPDLQSGNIGYKIAQRFGHFEAIGPILQGLNK 298

Query: 299 PVSDLSRGCNAEDVYKVSIITATQAL 324
           PVSDLSRG N EDVYK++IITA Q L
Sbjct: 299 PVSDLSRGSNEEDVYKLAIITAAQTL 324


Lambda     K      H
   0.315    0.133    0.369 

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: 366
Number of extensions: 16
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: 328
Length of database: 328
Length adjustment: 28
Effective length of query: 300
Effective length of database: 300
Effective search space:    90000
Effective search space used:    90000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_022528623.1 L248_RS03165 (phosphate acetyltransferase)
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00651.hmm
# target sequence database:        /tmp/gapView.2126843.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00651  [M=304]
Accession:   TIGR00651
Description: pta: phosphate acetyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-123  396.7   0.0   4.6e-123  396.5   0.0    1.0  1  NCBI__GCF_000469325.1:WP_022528623.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_022528623.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.5   0.0  4.6e-123  4.6e-123       1     304 []      18     320 ..      18     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.5 bits;  conditional E-value: 4.6e-123
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           iv+PEg+e+r++ Aa  l+ ++i++++ll+  +++++ +a++   +lg++++ dp+ + d +++v  ++++rk
  NCBI__GCF_000469325.1:WP_022528623.1  18 IVFPEGTEPRIIGAAVRLNAERILTPILLGTPAAVQA-AAEKAGFTLGNIQILDPQDYADFDSLVASFVDRRK 89 
                                           8******************************999998.999******************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee..e 144
                                            k  t+++ +++lrD+++++++lv++g adg+vsGav++t +t+rpalqiikt++gv+ +s+ fim+++   e
  NCBI__GCF_000469325.1:WP_022528623.1  90 GK-NTKEQGETMLRDPNYFGTMLVYTGLADGMVSGAVHSTGETVRPALQIIKTKPGVSRTSGAFIMQRGRdaE 161
                                           **.89999***********************************************************987669 PP

                             TIGR00651 145 vlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdll 217
                                           +++faDCa+++dPna+eLAeiA+ sa++ak ++ ++p+va+ls+stkgs+k+ +v+kv+eA+ki++e +pdl 
  NCBI__GCF_000469325.1:WP_022528623.1 162 RYIFADCAINIDPNAQELAEIAVASAQTAKLFD-IDPHVAMLSFSTKGSAKAPQVDKVVEATKIAHELAPDLD 233
                                           ********************************9.*************************************** PP

                             TIGR00651 218 ldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRG 290
                                           ldGelqfDaA+v++v ++kap s+vagka+vf+FPdL++GnigYki+qR++++eaiGPilqGl+kPv+DLsRG
  NCBI__GCF_000469325.1:WP_022528623.1 234 LDGELQFDAAFVPSVGAQKAPGSTVAGKATVFIFPDLQSGNIGYKIAQRFGHFEAIGPILQGLNKPVSDLSRG 306
                                           ************************************************************************* PP

                             TIGR00651 291 asvedivnvviita 304
                                           ++ ed+++++iita
  NCBI__GCF_000469325.1:WP_022528623.1 307 SNEEDVYKLAIITA 320
                                           ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (328 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.46
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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