GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Pseudomonas fluorescens GW456-L13

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate PfGW456L13_2177 Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)

Query= metacyc::BSU22620-MONOMER
         (360 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177
          Length = 370

 Score =  272 bits (696), Expect = 9e-78
 Identities = 150/356 (42%), Positives = 209/356 (58%), Gaps = 3/356 (0%)

Query: 7   LKQLKPYQPGKPIEAVKSEYGLD--KVVKLASNENPYGCSEAAKEALHHEIQQLALYPDG 64
           ++QL PY PGKP++ +  E  LD   ++KLASNENP G    A  A+   + +L  YPDG
Sbjct: 13  VQQLSPYVPGKPVDELARELDLDPASIIKLASNENPLGAGPKALAAIRDALAELTRYPDG 72

Query: 65  YSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVI 124
              AL++ L++   V    +  GNGS++I++++ RA+L    N V +   F  Y      
Sbjct: 73  NGFALKSLLAEQCRVELDQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIATQA 132

Query: 125 EGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSR 184
            GA+ + +  + D  HDL AML AID  T+VV+I +PNNPTGT+     L  FL+ VP  
Sbjct: 133 VGAQAKVVPAK-DWGHDLPAMLAAIDANTRVVFIANPNNPTGTWFDAEALDEFLQDVPEH 191

Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244
           VLVVLDEAY EY    D P+ +  L+ Y NL++ RTFSKAYGLAALRVGYG++   +   
Sbjct: 192 VLVVLDEAYIEYAEGSDLPDGLDFLAAYPNLLVSRTFSKAYGLAALRVGYGLSTAVVADV 251

Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304
           +   R+PFN + L  AAA AAL D+ ++A   + N +G+QQ     +  GL   PS+ NF
Sbjct: 252 LNRVRQPFNVNSLALAAACAALKDEEYLAQSRQLNESGMQQLEAGFRELGLSWIPSKGNF 311

Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360
           + +D  + A  +FQ LL +G IVR     G P  LRITIG   +N   L  L ++L
Sbjct: 312 ICVDLGQVAAPVFQGLLREGVIVRPVANYGMPNHLRITIGLPAENSRFLEALTKVL 367


Lambda     K      H
   0.317    0.134    0.382 

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: 376
Number of extensions: 14
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: 360
Length of database: 370
Length adjustment: 30
Effective length of query: 330
Effective length of database: 340
Effective search space:   112200
Effective search space used:   112200
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: 49 (23.5 bits)

Align candidate PfGW456L13_2177 (Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57))
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.2872174.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                           -----------
   8.7e-116  372.5   0.0   9.8e-116  372.4   0.0    1.0  1  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.4   0.0  9.8e-116  9.8e-116       2     348 ..      11     365 ..      10     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 372.4 bits;  conditional E-value: 9.8e-116
                                           TIGR01141   2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrY 52 
                                                         + +++l+pY+pg      arel  +   ++kL+snEnP+g  +k+++a++++l++l+rY
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177  11 PGVQQLSPYVPGkpvdelARELDLDpaSIIKLASNENPLGAGPKALAAIRDALAELTRY 69 
                                                         679***************999999999******************************** PP

                                           TIGR01141  53 pdpqalelkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYev 111
                                                         pd ++++lk+ la+++ ve ++++lgnGs++++el++ra+l pg +++++e+++++Y++
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177  70 PDGNGFALKSLLAEQCRVELDQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPI 128
                                                         *********************************************************** PP

                                           TIGR01141 112 sakiagaevkevplkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvle 170
                                                          +++ ga+ k vp+k++g +dl+a+l+a++ ++++vf+a+PnnPtG+++++e + ++l+
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 129 ATQAVGAQAKVVPAKDWG-HDLPAMLAAIDANTRVVFIANPNNPTGTWFDAEALDEFLQ 186
                                                         *************99995.9*************************************** PP

                                           TIGR01141 171 ev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgLAglRvGyaian 225
                                                          v e++lVV+DeAYie++e    ++ l++la ypnl+v+rT+SKa+gLA+lRvGy++++
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 187 DVpEHVLVVLDEAYIEYAEGsdlPDGLDFLAAYPNLLVSRTFSKAYGLAALRVGYGLST 245
                                                         **99**************999999*********************************** PP

                                           TIGR01141 226 aeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkklegle 284
                                                         a ++++l++vr+p+nv+slal+aa+aal+d+++++++ + +++++++l++++++l gl+
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 246 AVVADVLNRVRQPFNVNSLALAAACAALKDEEYLAQSRQLNESGMQQLEAGFREL-GLS 303
                                                         *******************************************************.8** PP

                                           TIGR01141 285 vyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerll 343
                                                         +++Sk+NF+ +++ + a+ +++ ll++g+ivR ++++ g+ +++lRit+G + en r+l
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 304 WIPSKGNFICVDLGQVAAPVFQGLLREGVIVRPVANY-GM-PNHLRITIGLPAENSRFL 360
                                                         *************************************.96.****************** PP

                                           TIGR01141 344 ealke 348
                                                         eal +
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 361 EALTK 365
                                                         **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (370 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: 23.46
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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