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.21461.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: 7.80
//
[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:

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:

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:

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:

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