Alignments for a candidate for pta in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Mycolicibacterium vanbaalenii PYR-1

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_011777975.1 MVAN_RS03535 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000015305.1:WP_011777975.1
          Length = 692

 Score =  388 bits (996), Expect = e-112
 Identities = 194/327 (59%), Positives = 251/327 (76%)

Query: 1   MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60
           ++ ++F + L+++AR++   IVLPEG+DDRIL AA +LL + + D+TILG+  +++ RA 
Sbjct: 366 VTPQMFTHQLIEQARSDRKRIVLPEGNDDRILKAAGRLLHRGVADLTILGEEAQVRARAA 425

Query: 61  ELGLHLNTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHNGD 120
           ELGL L+TA +++P T    + FAEQ+A+LR  K VT+++A EI+ D+SYFGTM+VHN  
Sbjct: 426 ELGLDLSTAVVLDPQTSELCDRFAEQYAKLRAHKGVTVEQAHEIIHDVSYFGTMLVHNDL 485

Query: 121 ADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQ 180
            DGMVSGA +TTAHTI+P+ +II+T P  S VSSIFLM L   + A+GDCA+ P+PTAEQ
Sbjct: 486 VDGMVSGACHTTAHTIRPALEIIRTAPGVSTVSSIFLMCLAHEVLAYGDCAIVPDPTAEQ 545

Query: 181 LGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPL 240
           L +IA+ SA+TAAQFGI+P+VA+LSYSTG SG G+DVD+   A    R   PEL V+GP+
Sbjct: 546 LADIAISSARTAAQFGIEPKVAMLSYSTGTSGTGADVDKVRKATELVRSRAPELLVEGPI 605

Query: 241 QFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGLNK 300
           Q+DAAV+P VA  KMPDS VAG A V IFPDL  GN  YK  QR+  A+A+GP+LQGLNK
Sbjct: 606 QYDAAVEPSVAMTKMPDSRVAGHATVLIFPDLNTGNNTYKAVQRSAGAIAIGPVLQGLNK 665

Query: 301 PVNDLSRGATVPDIVNTVAITAIQAGG 327
           PVNDLSRGA V DIVNTVAITAIQA G
Sbjct: 666 PVNDLSRGALVEDIVNTVAITAIQAQG 692


Lambda     K      H
   0.318    0.134    0.386 

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: 617
Number of extensions: 21
Number of successful extensions: 1
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: 329
Length of database: 692
Length adjustment: 33
Effective length of query: 296
Effective length of database: 659
Effective search space:   195064
Effective search space used:   195064
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011777975.1 MVAN_RS03535 (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.19063.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-129  416.2   0.1     6e-129  415.8   0.1    1.2  1  lcl|NCBI__GCF_000015305.1:WP_011777975.1  MVAN_RS03535 phosphate acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011777975.1  MVAN_RS03535 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.8   0.1    6e-129    6e-129       1     304 []     386     687 ..     386     687 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.8 bits;  conditional E-value: 6e-129
                                 TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 
                                               ivlPEg++ r+lkAa  l+++++a+ ++l++++++ + +a+e+ l+l++ vv dp++s+  ++++e++ 
  lcl|NCBI__GCF_000015305.1:WP_011777975.1 386 IVLPEGNDDRILKAAGRLLHRGVADLTILGEEAQVRA-RAAELGLDLSTAVVLDPQTSELCDRFAEQYA 453
                                               8****************************99988877.9****************************** PP

                                 TIGR00651  70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfi 138
                                               ++r hkGvt ++a+e ++D ++++++lv+ + +dg+vsGa +tta+t+rpal+ii+t++gv++vss+f+
  lcl|NCBI__GCF_000015305.1:WP_011777975.1 454 KLRAHKGVTVEQAHEIIHDVSYFGTMLVHNDLVDGMVSGACHTTAHTIRPALEIIRTAPGVSTVSSIFL 522
                                               ********************************************************************* PP

                                 TIGR00651 139 mekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvk 207
                                               m++ +evl ++DCa+++dP+ae+LA+iA++sa +a ++g +epkva+lsyst++sg g++v+kv++A++
  lcl|NCBI__GCF_000015305.1:WP_011777975.1 523 MCLAHEVLAYGDCAIVPDPTAEQLADIAISSARTAAQFG-IEPKVAMLSYSTGTSGTGADVDKVRKATE 590
                                               ***************************************.***************************** PP

                                 TIGR00651 208 ilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPi 276
                                               +++ ++p+ll++G++q+DaA+ ++va  k+p+s vag+a+v++FPdL++Gn++Yk+vqR+a+a aiGP+
  lcl|NCBI__GCF_000015305.1:WP_011777975.1 591 LVRSRAPELLVEGPIQYDAAVEPSVAMTKMPDSRVAGHATVLIFPDLNTGNNTYKAVQRSAGAIAIGPV 659
                                               ********************************************************************* PP

                                 TIGR00651 277 lqGlakPvnDLsRGasvedivnvviita 304
                                               lqGl+kPvnDLsRGa+vedivn+v+ita
  lcl|NCBI__GCF_000015305.1:WP_011777975.1 660 LQGLNKPVNDLSRGALVEDIVNTVAITA 687
                                               **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (692 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 22.87
//
[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