GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Pseudomonas fluorescens FW300-N2E2

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate Pf6N2E2_2519 Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519
          Length = 370

 Score =  275 bits (704), Expect = 1e-78
 Identities = 152/356 (42%), Positives = 211/356 (59%), Gaps = 3/356 (0%)

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

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

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

Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244
           VLVVLDEAY EY    D P+ +  L+ Y NL++ RTFSKAYGLA+LRVGYG++   +   
Sbjct: 192 VLVVLDEAYIEYAEGSDLPDGLDFLAAYPNLLVSRTFSKAYGLASLRVGYGLSTAVVADV 251

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

Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360
           + +D  R A  ++Q LL +G IVR     G P  LR+TIG   +N   L  L+++L
Sbjct: 312 ICVDLGRVAAPVYQGLLREGVIVRPVVNYGMPNHLRVTIGLPAENNRFLEALSKVL 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: 361
Number of extensions: 13
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 Pf6N2E2_2519 (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.3273235.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.3e-115  370.6   0.0   3.8e-115  370.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519  Biosynthetic Aromatic amino acid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519  Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.4   0.0  3.8e-115  3.8e-115       2     348 ..      11     365 ..      10     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 370.4 bits;  conditional E-value: 3.8e-115
                                      TIGR01141   2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqa 57 
                                                    + +++l+pY+pg      arel  +   +vkL+snEnP+g s+k+++a+++el++l+rYpd ++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519  11 PGVQQLSPYVPGkpvdelARELDLDpaSIVKLASNENPLGASPKALAAIRDELAELTRYPDGNG 74 
                                                    679***************999999999************************************* PP

                                      TIGR01141  58 lelkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevk 121
                                                    ++lk+ la+++gve ++++lgnGs++++el++ra+l pg +++++e+++++Y++ +++ ga+  
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519  75 FALKSLLAERCGVELNQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIATQAVGADAH 138
                                                    **************************************************************** PP

                                      TIGR01141 122 evplkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYi 184
                                                     vp+k++g +dl+a+l+a++ ++++vf+a+PnnPtG++++++ + ++l+ v +++lVV+DeAYi
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 139 VVPAKDWG-HDLPAMLAAIDANTRVVFIANPNNPTGTWFDAQALDDFLQDVpAHVLVVLDEAYI 201
                                                    ***99995.9*****************************************88*********** PP

                                      TIGR01141 185 eFsee...asvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvssla 245
                                                    e++e    ++ l++la ypnl+v+rT+SKa+gLA+lRvGy++++a ++++l++vr+p+nv+s a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 202 EYAEGsdlPDGLDFLAAYPNLLVSRTFSKAYGLASLRVGYGLSTAVVADVLNRVRQPFNVNSFA 265
                                                    ***999999******************************************************* PP

                                      TIGR01141 246 leaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvkedaeelleall 309
                                                    l+aa+aal+d+++++++ + +++++++l++++++l gl++++Sk+NF+ +++ + a+ +++ ll
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 266 LAAACAALQDEAYLAESRRLNAAGMQQLEAGFREL-GLSWIPSKGNFICVDLGRVAAPVYQGLL 328
                                                    ***********************************.8*************************** PP

                                      TIGR01141 310 ekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                                    ++g+ivR + ++ g+ +++lR+t+G + en+r+leal++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 329 REGVIVRPVVNY-GM-PNHLRVTIGLPAENNRFLEALSK 365
                                                    **********99.96.********************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.85
//
[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