Alignments for a candidate for pta in Crocosphaera subtropica ATCC 51142

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Crocosphaera subtropica ATCC 51142

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_009543586.1 CCE_RS26950 phosphate acetyltransferase

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



>NCBI__GCF_000017845.1:WP_009543586.1
          Length = 756

 Score =  253 bits (645), Expect = 1e-71
 Identities = 137/329 (41%), Positives = 203/329 (61%), Gaps = 7/329 (2%)

Query: 2   DLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNL 61
           ++I    + AK + K I+  EG+  + L A   +I+E +A+ +L+G  +KIK+K +EL L
Sbjct: 426 EIIRHSIQKAKTNPKSIVFPEGDNPKILKACQILIEERIAQPILIGSVDKIKQKITELGL 485

Query: 62  DISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDGM 121
           ++    I+DP    + + Y ++ + LR+ KGMT+ ++++ V DP  FA + ++ G  DGM
Sbjct: 486 ELDNVPIIDPLNFSERDYYIQELFALRQRKGMTLTQAKQSVLDPTIFALLIVQLGQADGM 545

Query: 122 VSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPTS 181
           V+G       +LR  LQII T   V   SG ++M+     Y       FAD  VN  PT+
Sbjct: 546 VAGVSQAYPSILRSALQIIGTKAEVNCASGVYLMLFKHRVY------FFADTTVNIEPTA 599

Query: 182 DELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAID 241
           + LADIA+ +A  A++L ++ P++AMLSFS  GS K  + D+VKNAV++ K  +PDL ID
Sbjct: 600 EILADIALESATLAKRL-DIVPRIAMLSFSNFGSVKHPLCDRVKNAVQLVKMRQPDLIID 658

Query: 242 GELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQG 301
           GE+Q D A++  + A   P S + GNAN+L+FPDLQ+GNI YKL+     A+AIGPI  G
Sbjct: 659 GEMQADTAVNPTLVAEHYPFSEIKGNANILIFPDLQSGNIAYKLLHELGGAEAIGPILLG 718

Query: 302 FAKPINDLSRGCSSEDIVNVVAITVVQAQ 330
             KPI+ L RGC    IVN+ AI V+ AQ
Sbjct: 719 MKKPIHILQRGCQINTIVNMSAIAVLDAQ 747


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: 495
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: 333
Length of database: 756
Length adjustment: 34
Effective length of query: 299
Effective length of database: 722
Effective search space:   215878
Effective search space used:   215878
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: 52 (24.6 bits)

Align candidate WP_009543586.1 CCE_RS26950 (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.1072188.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.5e-98  314.4   0.1    6.4e-98  313.9   0.1    1.2  1  NCBI__GCF_000017845.1:WP_009543586.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017845.1:WP_009543586.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.9   0.1   6.4e-98   6.4e-98       1     303 [.     442     742 ..     442     743 .. 0.99

  Alignments for each domain:
  == domain 1  score: 313.9 bits;  conditional E-value: 6.4e-98
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           iv+PEg+++++lkA ++l+e++ia+++l+++ +++++ k++e+ l+l +v ++dp  + +++ y+++l+ +r+
  NCBI__GCF_000017845.1:WP_009543586.1 442 IVFPEGDNPKILKACQILIEERIAQPILIGSVDKIKQ-KITELGLELDNVPIIDPLNFSERDYYIQELFALRQ 513
                                           8****************************99999988.9********************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                            kG+t+++a++ + D++ +a l+v+lg+adg+v+G  ++  ++lr+alqii+t+  v+++s+v++m  +++v+
  NCBI__GCF_000017845.1:WP_009543586.1 514 RKGMTLTQAKQSVLDPTIFALLIVQLGQADGMVAGVSQAYPSILRSALQIIGTKAEVNCASGVYLMLFKHRVY 586
                                           ************************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           +faD +v+++P+ae LA+iAl+sa  ak l+ + p++a+ls+s  gs k    ++vk+Av+++k ++pdl +d
  NCBI__GCF_000017845.1:WP_009543586.1 587 FFADTTVNIEPTAEILADIALESATLAKRLD-IVPRIAMLSFSNFGSVKHPLCDRVKNAVQLVKMRQPDLIID 658
                                           ******************************9.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           Ge+q D+A+ +++ ++  p se++g+an+++FPdL++Gni+Yk+ + l++aeaiGPil+G++kP+  L RG++
  NCBI__GCF_000017845.1:WP_009543586.1 659 GEMQADTAVNPTLVAEHYPFSEIKGNANILIFPDLQSGNIAYKLLHELGGAEAIGPILLGMKKPIHILQRGCQ 731
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviit 303
                                           ++ ivn+++i 
  NCBI__GCF_000017845.1:WP_009543586.1 732 INTIVNMSAIA 742
                                           *******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (756 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: 43.46
//
[ok]

This GapMind analysis is from Apr 09 2024. 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