Alignments for a candidate for pta in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Calditerrivibrio nitroreducens DSM 19672

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_013450890.1 CALNI_RS03825 phosphate acetyltransferase

Query= metacyc::PTACLOS-MONOMER
         (333 letters)



>NCBI__GCF_000183405.1:WP_013450890.1
          Length = 328

 Score =  320 bits (820), Expect = 3e-92
 Identities = 165/329 (50%), Positives = 222/329 (67%), Gaps = 1/329 (0%)

Query: 1   MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60
           M L+E  WE AKQ +K I+L EG ++R + AA  I++  LA+++++GDE KI+       
Sbjct: 1   MPLMEKFWEMAKQRQKTIVLPEGHDERTIDAAHTIVQNKLAKIIVLGDEQKIESLFKAKG 60

Query: 61  LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDG 120
             IS  EI++P TS     +A  +Y  RK KG++ E++   ++D LYF  M ++     G
Sbjct: 61  YPIS-CEIINPTTSKYLNDFASAYYNKRKSKGISEEEALNCMKDILYFGAMLVEQDIAQG 119

Query: 121 MVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPT 180
            V+GA +TT D+LR  +++I T PG+  VS  F+M+    ++G++G +LFADCAVNPNP 
Sbjct: 120 CVTGACNTTADVLRAAIRVIGTKPGINTVSSCFIMVTNKKEFGKDGAILFADCAVNPNPD 179

Query: 181 SDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAI 240
           S +LA+IA+ TA++ R     EP+VAMLSFST GSA+   +DKV  A++I K+  PDL I
Sbjct: 180 SRQLAEIAVATADSCRAFLEEEPRVAMLSFSTKGSAQHPDIDKVLEALKIAKEISPDLMI 239

Query: 241 DGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQ 300
           DGE+Q DAA+   V   KAP SNVAG ANVL+FPDL  GNI YKLV+R A A+AIGPI Q
Sbjct: 240 DGEMQADAALIKAVGEKKAPGSNVAGKANVLIFPDLDAGNIAYKLVERIAGAEAIGPIIQ 299

Query: 301 GFAKPINDLSRGCSSEDIVNVVAITVVQA 329
           G  KP+NDLSRGC   DIVNV AIT VQA
Sbjct: 300 GLRKPVNDLSRGCKYMDIVNVAAITAVQA 328


Lambda     K      H
   0.316    0.134    0.374 

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: 313
Number of extensions: 14
Number of successful extensions: 4
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: 333
Length of database: 328
Length adjustment: 28
Effective length of query: 305
Effective length of database: 300
Effective search space:    91500
Effective search space used:    91500
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_013450890.1 CALNI_RS03825 (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.28933.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-123  398.0   1.1   1.8e-123  397.8   1.1    1.0  1  lcl|NCBI__GCF_000183405.1:WP_013450890.1  CALNI_RS03825 phosphate acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183405.1:WP_013450890.1  CALNI_RS03825 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.8   1.1  1.8e-123  1.8e-123       1     304 []      18     325 ..      18     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 397.8 bits;  conditional E-value: 1.8e-123
                                 TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 
                                               ivlPEg++er+++Aa++++++k+a+ ++l++++++++  +k     + ++++++p++sk +++++ ++y
  lcl|NCBI__GCF_000183405.1:WP_013450890.1  18 IVLPEGHDERTIDAAHTIVQNKLAKIIVLGDEQKIES-LFKAKGYPI-SCEIINPTTSKYLNDFASAYY 84 
                                               8******************************999999.444444444.56788999999********** PP

                                 TIGR00651  70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfi 138
                                               +krk kG++e+ea + ++D ++++a+lve++ a+g+v+Ga +tta++lr+a+++i+t++g+++vss+fi
  lcl|NCBI__GCF_000183405.1:WP_013450890.1  85 NKRKSKGISEEEALNCMKDILYFGAMLVEQDIAQGCVTGACNTTADVLRAAIRVIGTKPGINTVSSCFI 153
                                               ********************************************************************* PP

                                 TIGR00651 139 mekee......evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevek 201
                                               m +++      + ++faDCav+++P++++LAeiA+ +a+s++++ eeep+va+ls+stkgs++  +++k
  lcl|NCBI__GCF_000183405.1:WP_013450890.1 154 MVTNKkefgkdGAILFADCAVNPNPDSRQLAEIAVATADSCRAFLEEEPRVAMLSFSTKGSAQHPDIDK 222
                                               ***99999999999******************************************************* PP

                                 TIGR00651 202 vkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRlada 270
                                               v eA+ki+ke  pdl++dGe+q DaAl++ v ekkap s+vagkanv++FPdLdaGni+Yk+v+R+a+a
  lcl|NCBI__GCF_000183405.1:WP_013450890.1 223 VLEALKIAKEISPDLMIDGEMQADAALIKAVGEKKAPGSNVAGKANVLIFPDLDAGNIAYKLVERIAGA 291
                                               ********************************************************************* PP

                                 TIGR00651 271 eaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                               eaiGPi+qGl+kPvnDLsRG++  divnv++ita
  lcl|NCBI__GCF_000183405.1:WP_013450890.1 292 EAIGPIIQGLRKPVNDLSRGCKYMDIVNVAAITA 325
                                               ********************************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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.00
//
[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 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