GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Phaeobacter inhibens BS107

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate GFF1745 PGA1_c17690 serine acetyltransferase CysE

Query= BRENDA::C4IRW0
         (281 letters)



>FitnessBrowser__Phaeo:GFF1745
          Length = 271

 Score =  297 bits (761), Expect = 1e-85
 Identities = 142/261 (54%), Positives = 189/261 (72%)

Query: 20  LDQVDPIWHSIRAEAEEATRNDPVLGAFLYATILNQPSLEEAVMHRIAERLGHPDVSADI 79
           +  VDP+W  I  EA++A R  P++G  ++A IL+  SLE+A+ +RIA +L   ++S  I
Sbjct: 8   VSSVDPVWDQITTEAQDAVRRQPLMGGLIHACILHHTSLEKALSYRIAAKLCSNEMSMVI 67

Query: 80  LRQTFDTMLEANPEWSHVLRVDIQAVYDRDPAYSRFMDPVLYLKGFHAIQTHRLAHWLYK 139
           LR+  D     NP+     R D+ AVY+RDPA  R + P+LY KG+ A+Q +R+AHWL++
Sbjct: 68  LREIVDKAYGENPDLIAAGRADLMAVYERDPACHRLLQPILYFKGYQAVQAYRVAHWLWQ 127

Query: 140 QGRKDFAYYLQSRSSSIFQTDIHPAARLGSGLFLDHATGLVVGETAVVEDNVSILHGVTL 199
           +G  D +Y+ Q R S IF  DIHPAA++G G+ +DHA  +V+GETAVV DNVS+LH VTL
Sbjct: 128 KGDYDLSYFFQMRISEIFGVDIHPAAKIGRGIMIDHAHSIVIGETAVVGDNVSMLHSVTL 187

Query: 200 GGTGKSSGDRHPKIRQGVLIGAGAKILGNIQVGQCSKIAAGSVVLKSVPHNVTVAGVPAR 259
           GGTGK   DRHPKI  GVLIGAGAK+LGNI+VG CS+IAAGSVVL+ +P   TVAGVPA+
Sbjct: 188 GGTGKEEEDRHPKIGDGVLIGAGAKVLGNIKVGHCSRIAAGSVVLQEIPPCKTVAGVPAK 247

Query: 260 IIGETGCTEPSRVMDQMLGDG 280
           I+GE GC +PS  M+Q+LG G
Sbjct: 248 IVGEAGCDQPSVSMNQVLGGG 268


Lambda     K      H
   0.320    0.135    0.403 

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: 282
Number of extensions: 10
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: 281
Length of database: 271
Length adjustment: 25
Effective length of query: 256
Effective length of database: 246
Effective search space:    62976
Effective search space used:    62976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate GFF1745 PGA1_c17690 (serine acetyltransferase CysE)
to HMM TIGR01172 (cysE: serine O-acetyltransferase (EC 2.3.1.30))

# 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.aa/TIGR01172.hmm
# target sequence database:        /tmp/gapView.22722.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01172  [M=162]
Accession:   TIGR01172
Description: cysE: serine O-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.2e-72  229.3   1.1    4.4e-72  227.5   0.5    1.8  2  lcl|FitnessBrowser__Phaeo:GFF1745  PGA1_c17690 serine acetyltransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1745  PGA1_c17690 serine acetyltransferase CysE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.037     0.037       7      47 ..      24      65 ..      18      74 .. 0.73
   2 !  227.5   0.5   4.4e-72   4.4e-72       3     162 .]      88     247 ..      86     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.037
                          TIGR01172  7 avlerDPaaesal.evlllykglhallayrlahalykrklkl 47
                                        +++r P +   +   +l +++l   l+yr+a++l ++++ +
  lcl|FitnessBrowser__Phaeo:GFF1745 24 DAVRRQPLMGGLIhACILHHTSLEKALSYRIAAKLCSNEMSM 65
                                       5566777666554156788899999999***99998887765 PP

  == domain 2  score: 227.5 bits;  conditional E-value: 4.4e-72
                          TIGR01172   3 edlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliDh 78 
                                        +dl av+erDPa+++ l+++l++kg++a++ayr+ah+l++++ + l+++++ +++ ++gvdihPaakigrg++iDh
  lcl|FitnessBrowser__Phaeo:GFF1745  88 ADLMAVYERDPACHRLLQPILYFKGYQAVQAYRVAHWLWQKGDYDLSYFFQMRISEIFGVDIHPAAKIGRGIMIDH 163
                                        799************************************************************************* PP

                          TIGR01172  79 atGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpaea 154
                                        a+ +viGetav+gd+vs++++vtLGgtgke+ +RhP++++gv+igagakvLGni+vg+ ++i a+svvl+++p+  
  lcl|FitnessBrowser__Phaeo:GFF1745 164 AHSIVIGETAVVGDNVSMLHSVTLGGTGKEEEDRHPKIGDGVLIGAGAKVLGNIKVGHCSRIAAGSVVLQEIPPCK 239
                                        **************************************************************************** PP

                          TIGR01172 155 tvvGvpar 162
                                        tv+Gvpa+
  lcl|FitnessBrowser__Phaeo:GFF1745 240 TVAGVPAK 247
                                        ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (162 nodes)
Target sequences:                          1  (271 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: 9.15
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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