Alignments for a candidate for pta in Lactobacillus oryzae SG293

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Lactobacillus oryzae SG293

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_034529140.1 LOSG293_RS08105 phosphate acetyltransferase

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



>NCBI__GCF_000740055.1:WP_034529140.1
          Length = 324

 Score =  419 bits (1077), Expect = e-122
 Identities = 212/324 (65%), Positives = 256/324 (79%), Gaps = 3/324 (0%)

Query: 1   MDLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALN 60
           M+LF+SLK KIK +K  LVFPEGEDERI+ A  RLA D L  P++LGN A+++K A   N
Sbjct: 1   MELFDSLKEKIKTKKQTLVFPEGEDERIVGATVRLAADGLVNPIVLGNPAQVEKLAQDHN 60

Query: 61  VSLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVD 120
            +LDG++++D +    EV   M Q+++ERR GK TA+Q A+ L+DPNY GT +VYM   D
Sbjct: 61  WNLDGVQVIDPK---AEVDDAMRQSLLERRNGKNTAEQVAKMLEDPNYVGTMLVYMGRAD 117

Query: 121 GMVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLA 180
           GMVSGA HPTGDTVRPALQIIKTKPGV  ISG+F+MQKGD+RY+FADCAINI  +   +A
Sbjct: 118 GMVSGANHPTGDTVRPALQIIKTKPGVKRISGAFIMQKGDERYVFADCAINIELDAAGMA 177

Query: 181 EIAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQF 240
           E+ +ES  TA++F IDP+VALLSFST GSAK   V KV  A +LA++  P +PIDGE+QF
Sbjct: 178 EVGIESANTAKVFGIDPKVALLSFSTKGSAKGDMVTKVQEAAELAKQQAPDLPIDGELQF 237

Query: 241 DAAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPV 300
           DAAFVP+V + K   S VAGHATVFVFPELQSGNIGYKIAQR GG+EAIGPILQGLN+PV
Sbjct: 238 DAAFVPSVGEKKAPGSNVAGHATVFVFPELQSGNIGYKIAQRFGGYEAIGPILQGLNQPV 297

Query: 301 SDLSRGCNAEDVYKVSIITATQAL 324
           SDLSRG N EDVYKV+IITA QA+
Sbjct: 298 SDLSRGANEEDVYKVAIITAAQAV 321


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: 383
Number of extensions: 8
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: 328
Length of database: 324
Length adjustment: 28
Effective length of query: 300
Effective length of database: 296
Effective search space:    88800
Effective search space used:    88800
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: 48 (23.1 bits)

Align candidate WP_034529140.1 LOSG293_RS08105 (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.2102676.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-116  374.0   0.0   3.8e-116  373.8   0.0    1.0  1  NCBI__GCF_000740055.1:WP_034529140.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000740055.1:WP_034529140.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.8   0.0  3.8e-116  3.8e-116       1     304 []      18     317 ..      18     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 373.8 bits;  conditional E-value: 3.8e-116
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           +v+PEg++er++ A   la  +++++++l+n ++++k  a++ n +l  v+v+dp+     +   + l e+r 
  NCBI__GCF_000740055.1:WP_034529140.1  18 LVFPEGEDERIVGATVRLAADGLVNPIVLGNPAQVEK-LAQDHNWNLDGVQVIDPKAE-VDDAMRQSLLERRN 88 
                                           69********************************999.99****************99.66889999****** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                            k  t ++++++l+D+++++++lv++g adg+vsGa + t +t+rpalqiikt++gvk +s+ fim+k++e++
  NCBI__GCF_000740055.1:WP_034529140.1  89 GK-NTAEQVAKMLEDPNYVGTMLVYMGRADGMVSGANHPTGDTVRPALQIIKTKPGVKRISGAFIMQKGDERY 160
                                           **.77888899************************************************************** PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           vfaDCa++++ +a  +Ae+ ++sa++ak +g ++pkvalls+stkgs+kg++v kv+eA +++k+++pdl +d
  NCBI__GCF_000740055.1:WP_034529140.1 161 VFADCAINIELDAAGMAEVGIESANTAKVFG-IDPKVALLSFSTKGSAKGDMVTKVQEAAELAKQQAPDLPID 232
                                           *******************************.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           GelqfDaA+v++v ekkap s+vag+a+vfvFP+L++GnigYki+qR++++eaiGPilqGl++Pv+DLsRGa+
  NCBI__GCF_000740055.1:WP_034529140.1 233 GELQFDAAFVPSVGEKKAPGSNVAGHATVFVFPELQSGNIGYKIAQRFGGYEAIGPILQGLNQPVSDLSRGAN 305
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                            ed+++v+iita
  NCBI__GCF_000740055.1:WP_034529140.1 306 EEDVYKVAIITA 317
                                           **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (324 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: 25.59
//
[ok]

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources