GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisC in Pseudomonas fluorescens FW300-N1B4

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Pf1N1B4_349 Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)

Query= curated2:Q9RI00
         (366 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 Biosynthetic Aromatic
           amino acid aminotransferase beta (EC 2.6.1.57)
          Length = 370

 Score =  437 bits (1125), Expect = e-127
 Identities = 232/371 (62%), Positives = 276/371 (74%), Gaps = 11/371 (2%)

Query: 1   MSADFLALAVPGVQKLSPYVTGKPIDELARELGIEPARIVKLASNENPLGPNPRVLEAVR 60
           MS +FLALA PGVQ+LSPYV GKP+DELAREL ++PA IVKLASNENPLG +P+ L A+R
Sbjct: 1   MSGNFLALAQPGVQQLSPYVPGKPVDELARELNLDPANIVKLASNENPLGASPKALAAIR 60

Query: 61  GELSELTRYPDGSGFRLKAKLAERFGLKSEQITLGNGSNDIIDLVARC-CGAGPNAVFSA 119
             L+ELTRYPDG+GF LK  LA++  ++  Q+TLGNGSNDI++LVAR     G NAVFSA
Sbjct: 61  EALTELTRYPDGNGFALKTLLADQCRVELNQVTLGNGSNDILELVARAYLAPGLNAVFSA 120

Query: 120 HAFAAYPLCTQAAGAESRVVPAVDYGHDLDGMLKAIDEQTAVIFIANPNNPTGNLVRAQA 179
           HAFA YP+ TQA GA+++V+PA D+GHDL  ML AID  T V+FIANPNNPTG    AQA
Sbjct: 121 HAFAVYPIVTQAVGAQAKVIPAKDWGHDLSAMLAAIDADTRVVFIANPNNPTGTWFDAQA 180

Query: 180 LESFLDRVPERVLVVLDEAYIEFYRGTNC-QRLNYLVRYPNLLVSRTLSKVYGLAGLRVG 238
           L+ FL  VP  VLVVLDEAYIE+  G++    L+YL  YPNLLVSRT SK YGLA LRVG
Sbjct: 181 LDDFLQDVPAHVLVVLDEAYIEYAEGSDLPDGLDYLAAYPNLLVSRTFSKAYGLASLRVG 240

Query: 239 YSASSPQIADVLNRVRQPFNVNSLALVAACAG-----WMTSSIWLKGGGWIAPVWELEQG 293
           Y  SS  +ADVLNRVRQPFNVNSLAL AACA      ++  S  L   G    + +L+ G
Sbjct: 241 YGLSSAIVADVLNRVRQPFNVNSLALAAACAALQDVEYLAESRRLNESG----MQQLQAG 296

Query: 294 LAELRLKWIPSRGNFLAVDLGRDAAPINAGLLRDGVIVRPIAGYDCPTFLRVSIGTEQEN 353
             EL L WIPS+GNF+ VDLGR AAP+  GLLR+GVIVRP+A Y  P  LR++IG   EN
Sbjct: 297 FRELGLSWIPSKGNFICVDLGRVAAPVFEGLLREGVIVRPVANYGMPNHLRITIGLPAEN 356

Query: 354 ARFLEALRVVL 364
           +RFLEAL  V+
Sbjct: 357 SRFLEALTKVM 367


Lambda     K      H
   0.320    0.138    0.412 

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: 455
Number of extensions: 21
Number of successful extensions: 4
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: 366
Length of database: 370
Length adjustment: 30
Effective length of query: 336
Effective length of database: 340
Effective search space:   114240
Effective search space used:   114240
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: 49 (23.5 bits)

Align candidate Pf1N1B4_349 (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.19915.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   7.2e-116  372.8   0.0   8.2e-116  372.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349  Biosynthetic Aromatic amino acid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349  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 !  372.6   0.0  8.2e-116  8.2e-116       2     348 ..      11     365 ..      10     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 372.6 bits;  conditional E-value: 8.2e-116
                                     TIGR01141   2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqal 58 
                                                   + +++l+pY+pg      arel  +  ++vkL+snEnP+g s+k+++a++e+l++l+rYpd +++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349  11 PGVQQLSPYVPGkpvdelARELNLDpaNIVKLASNENPLGASPKALAAIREALTELTRYPDGNGF 75 
                                                   679***************999999999************************************** PP

                                     TIGR01141  59 elkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkev 123
                                                   +lk+ la+++ ve ++++lgnGs++++el++ra+l pg +++++ +++++Y++++++ ga+ k +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349  76 ALKTLLADQCRVELNQVTLGNGSNDILELVARAYLAPGLNAVFSAHAFAVYPIVTQAVGAQAKVI 140
                                                   ***************************************************************** PP

                                     TIGR01141 124 plkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFs 187
                                                   p+k++g +dl a+l+a++ ++++vf+a+PnnPtG++++++ + ++l+ v +++lVV+DeAYie++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 141 PAKDWG-HDLSAMLAAIDADTRVVFIANPNNPTGTWFDAQALDDFLQDVpAHVLVVLDEAYIEYA 204
                                                   *99995.9*****************************************88************** PP

                                     TIGR01141 188 ee...asvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaa 249
                                                   e    ++ l++la ypnl+v+rT+SKa+gLA+lRvGy++++a ++++l++vr+p+nv+slal+aa
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 205 EGsdlPDGLDYLAAYPNLLVSRTFSKAYGLASLRVGYGLSSAIVADVLNRVRQPFNVNSLALAAA 269
                                                   999999*********************************************************** PP

                                     TIGR01141 250 vaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgii 314
                                                   +aal+d ++++++ + +++++++l++++++l gl++++Sk+NF+ +++ + a+ ++e ll++g+i
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 270 CAALQDVEYLAESRRLNESGMQQLQAGFREL-GLSWIPSKGNFICVDLGRVAAPVFEGLLREGVI 333
                                                   *******************************.8******************************** PP

                                     TIGR01141 315 vRdlksaeglleeclRitvGtreenerllealke 348
                                                   vR ++++ g+ +++lRit+G + en r+leal +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 334 VRPVANY-GM-PNHLRITIGLPAENSRFLEALTK 365
                                                   *******.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: 8.35
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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