Alignments for a candidate for pta in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Dinoroseobacter shibae DFL-12

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 3608428 Dshi_1825 phosphate acetyltransferase (RefSeq)

Query= BRENDA::Q5LMK3
         (337 letters)



>FitnessBrowser__Dino:3608428
          Length = 341

 Score =  333 bits (855), Expect = 3e-96
 Identities = 183/327 (55%), Positives = 223/327 (68%), Gaps = 1/327 (0%)

Query: 6   PIDLLLSDPPARRATVALSEGSDPRVVAGALAAHSAGIADVILVGQAAEIRAAL-KAQGA 64
           P+ ++L++       +ALSEG DPRVVA A+ A    +A V+LVG  A I A L +A GA
Sbjct: 3   PLQMILANAARSDRKIALSEGEDPRVVAAAVQARKQRVARVVLVGDRATIVARLAEAGGA 62

Query: 65  PADSLTIHDPDSSPLTAEFAAAYYGLRRHKGVSEAAALAAVRTPLVYAAMLVRGDHAVGT 124
             D + +HDP      AE AA Y+ LR+HKGV+EA A AA+  P VYAA+LVR  HA GT
Sbjct: 63  ELDGIDVHDPREDLHRAEMAATYHQLRKHKGVTEADAEAAILNPHVYAALLVRLGHADGT 122

Query: 125 VGGAVATTSDVVRTAIQVIGAAPGAAMVSSFFLMYPPEAATAHARAMLYSDSGLVIDPSV 184
           +GGA ATT+++VRTAIQVIG APGA MVSSFFLM   +        ++++D+GLVIDP+ 
Sbjct: 123 LGGATATTAEIVRTAIQVIGTAPGAKMVSSFFLMLLCKDHHEKKGGLVFADAGLVIDPTA 182

Query: 185 AELAAIAAASAASCRALLRAEPKIAMLSFSTKGSARHPHVSKVTDALARLRADHPDLDAD 244
           AE+A I  ASAAS   L    P++AMLSFST+GSA    VSKV +A    R   P++  D
Sbjct: 183 AEMAEIGRASAASLVQLTGETPRVAMLSFSTRGSASGDKVSKVVEATEIFRQLAPEVTVD 242

Query: 245 GELQFDAAFVPSVGASKAPGSDVAGQANVMIFPNLDAGNIGYKITQRLGGYTAIGPVLQG 304
           GELQFDAAFVP V  +KAP S + G ANV +FPNLD GNI YKI QR+GG  AIGP+LQG
Sbjct: 243 GELQFDAAFVPEVATAKAPDSAIGGSANVFVFPNLDTGNIAYKIAQRIGGAVAIGPILQG 302

Query: 305 LAKPANDLSRGCVAGDVTQMIAVTVLQ 331
           LA PANDLSRGC A DV  MIA T  Q
Sbjct: 303 LALPANDLSRGCSAEDVLHMIATTAAQ 329


Lambda     K      H
   0.317    0.130    0.362 

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: 268
Number of extensions: 12
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: 337
Length of database: 341
Length adjustment: 28
Effective length of query: 309
Effective length of database: 313
Effective search space:    96717
Effective search space used:    96717
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: 49 (23.5 bits)

Align candidate 3608428 Dshi_1825 (phosphate acetyltransferase (RefSeq))
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.12368.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.5e-106  340.2   0.1   7.4e-106  340.0   0.1    1.0  1  lcl|FitnessBrowser__Dino:3608428  Dshi_1825 phosphate acetyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608428  Dshi_1825 phosphate acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.0   0.1  7.4e-106  7.4e-106       1     304 []      18     327 ..      18     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 340.0 bits;  conditional E-value: 7.4e-106
                         TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkGv 77 
                                       i l Eg+++rv+ Aa +  ++++a+ vl+++ +++v+  a+    +l  + v+dp+   ++ + + +++++rkhkGv
  lcl|FitnessBrowser__Dino:3608428  18 IALSEGEDPRVVAAAVQARKQRVARVVLVGDRATIVARLAEAGGAELDGIDVHDPREDLHRAEMAATYHQLRKHKGV 94 
                                       6689************************999999999999999********************************** PP

                         TIGR00651  78 tekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee......evlvf 148
                                       te+ a+ ++ ++ ++aallv+lg+adg+  Ga  tta+++r+a+q+i+t++g k+vss+f+m + +      + lvf
  lcl|FitnessBrowser__Dino:3608428  95 TEADAEAAILNPHVYAALLVRLGHADGTLGGATATTAEIVRTAIQVIGTAPGAKMVSSFFLMLLCKdhhekkGGLVF 171
                                       **************************************************************987777888899*** PP

                         TIGR00651 149 aDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfD 225
                                       aD  +++dP+a e+Aei   sa+s  +l++e p+va+ls+st+gs++g++v kv+eA++i+++ +p++++dGelqfD
  lcl|FitnessBrowser__Dino:3608428 172 ADAGLVIDPTAAEMAEIGRASAASLVQLTGETPRVAMLSFSTRGSASGDKVSKVVEATEIFRQLAPEVTVDGELQFD 248
                                       ***************************************************************************** PP

                         TIGR00651 226 aAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvvii 302
                                       aA+v++va+ kap+s++ g+anvfvFP+Ld+Gni+Yki+qR+++a aiGPilqGla P nDLsRG+s+ed++++++ 
  lcl|FitnessBrowser__Dino:3608428 249 AAFVPEVATAKAPDSAIGGSANVFVFPNLDTGNIAYKIAQRIGGAVAIGPILQGLALPANDLSRGCSAEDVLHMIAT 325
                                       *************************************************************************9998 PP

                         TIGR00651 303 ta 304
                                       ta
  lcl|FitnessBrowser__Dino:3608428 326 TA 327
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (341 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: 00:00:00.01
# Mc/sec: 7.14
//
[ok]

This GapMind analysis is from Sep 17 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