Alignments for a candidate for pta in Pontibacillus litoralis JSM 072002

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Pontibacillus litoralis JSM 072002

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_036834475.1 N784_RS09685 phosphate acetyltransferase

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



>NCBI__GCF_000775615.1:WP_036834475.1
          Length = 323

 Score =  389 bits (1000), Expect = e-113
 Identities = 194/323 (60%), Positives = 248/323 (76%), Gaps = 2/323 (0%)

Query: 2   DLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALNV 61
           +LF++L+SK+     K+V PEG DERI++AAS+L  + +  PVL+GN+ EI + A  L V
Sbjct: 3   NLFDTLRSKLSGTSKKIVLPEGLDERILTAASKLVQEGIITPVLIGNKDEITQKATELGV 62

Query: 62  SLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVDG 121
            + G EI+D      E   +MV + VERRKGK T ++A + L D NYFGT +VYM+  DG
Sbjct: 63  DVSGAEIIDPHTY--EAFDEMVASFVERRKGKATEEKAREMLTDENYFGTMLVYMNKADG 120

Query: 122 MVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLAE 181
           +VSGAAH T DTVRPALQIIKTKPG+   SG F+M + D++Y FADCAIN++P+   LAE
Sbjct: 121 LVSGAAHSTADTVRPALQIIKTKPGIKKTSGIFIMVRDDEKYAFADCAINMDPDSQDLAE 180

Query: 182 IAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQFD 241
           IA+ S +TA LFDIDPRVA+LSFST GSAKSP+ EKV  A ++A+E  P + +DGE QFD
Sbjct: 181 IALASAETAELFDIDPRVAMLSFSTKGSAKSPDTEKVVEAVQIAKEQKPELKLDGEFQFD 240

Query: 242 AAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPVS 301
           AAFVPAVA+ K  +S++ G A VFVFP L++GNIGYKIAQRMGGF+A+GP+LQGLN PV+
Sbjct: 241 AAFVPAVAEKKAPNSELKGDANVFVFPSLEAGNIGYKIAQRMGGFDAVGPVLQGLNAPVN 300

Query: 302 DLSRGCNAEDVYKVSIITATQAL 324
           DLSRGC+AEDVYK+SIITA Q+L
Sbjct: 301 DLSRGCSAEDVYKLSIITAAQSL 323


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: 358
Number of extensions: 12
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: 323
Length adjustment: 28
Effective length of query: 300
Effective length of database: 295
Effective search space:    88500
Effective search space used:    88500
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_036834475.1 N784_RS09685 (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.890502.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.1e-132  425.6   0.3   6.9e-132  425.5   0.3    1.0  1  NCBI__GCF_000775615.1:WP_036834475.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000775615.1:WP_036834475.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.5   0.3  6.9e-132  6.9e-132       1     304 []      19     319 ..      19     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: 425.5 bits;  conditional E-value: 6.9e-132
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEg +er+l Aa++l++++i+++vl++nk+e+++ ka+e+  +++  +++dp++++  ++ v  ++e+rk
  NCBI__GCF_000775615.1:WP_036834475.1  19 IVLPEGLDERILTAASKLVQEGIITPVLIGNKDEITQ-KATELGVDVSGAEIIDPHTYEAFDEMVASFVERRK 90 
                                           8*****************************9999999.9********************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                            k +te++are+l+De++++++lv++++adglvsGa+++ta+t+rpalqiikt++g+k +s++fim +++e +
  NCBI__GCF_000775615.1:WP_036834475.1  91 GK-ATEEKAREMLTDENYFGTMLVYMNKADGLVSGAAHSTADTVRPALQIIKTKPGIKKTSGIFIMVRDDEKY 162
                                           **.999******************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                            faDCa+++dP++++LAeiAl sa++a+ ++ ++p+va+ls+stkgs+k+ ++ekv+eAv+i+ke++p+l+ld
  NCBI__GCF_000775615.1:WP_036834475.1 163 AFADCAINMDPDSQDLAEIALASAETAELFD-IDPRVAMLSFSTKGSAKSPDTEKVVEAVQIAKEQKPELKLD 234
                                           *****************************99.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           Ge+qfDaA+v+ vaekkap+se++g+anvfvFP+L+aGnigYki+qR+++++a+GP+lqGl+ PvnDLsRG+s
  NCBI__GCF_000775615.1:WP_036834475.1 235 GEFQFDAAFVPAVAEKKAPNSELKGDANVFVFPSLEAGNIGYKIAQRMGGFDAVGPVLQGLNAPVNDLSRGCS 307
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                           +ed+++++iita
  NCBI__GCF_000775615.1:WP_036834475.1 308 AEDVYKLSIITA 319
                                           **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (323 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: 18.30
//
[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