GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Azospirillum brasilense Sp245

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate AZOBR_RS03845 AZOBR_RS03845 histidinol-phosphate phosphatase

Query= reanno::azobra:AZOBR_RS03845
         (260 letters)



>FitnessBrowser__azobra:AZOBR_RS03845
          Length = 260

 Score =  525 bits (1352), Expect = e-154
 Identities = 260/260 (100%), Positives = 260/260 (100%)

Query: 1   MTEPCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEA 60
           MTEPCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEA
Sbjct: 1   MTEPCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEA 60

Query: 61  ERPDDGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQ 120
           ERPDDGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQ
Sbjct: 61  ERPDDGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQ 120

Query: 121 PIVRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAK 180
           PIVRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAK
Sbjct: 121 PIVRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAK 180

Query: 181 VSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSG 240
           VSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSG
Sbjct: 181 VSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSG 240

Query: 241 RVVAAGDARTHRETLAALAG 260
           RVVAAGDARTHRETLAALAG
Sbjct: 241 RVVAAGDARTHRETLAALAG 260


Lambda     K      H
   0.320    0.139    0.424 

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: 472
Number of extensions: 18
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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 AZOBR_RS03845 AZOBR_RS03845 (histidinol-phosphate phosphatase)
to HMM TIGR02067 (hisN: histidinol-phosphatase (EC 3.1.3.15))

# 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/TIGR02067.hmm
# target sequence database:        /tmp/gapView.13310.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02067  [M=252]
Accession:   TIGR02067
Description: his_9_HisN: histidinol-phosphatase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.5e-95  304.2   0.0    3.9e-95  304.1   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS03845  AZOBR_RS03845 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS03845  AZOBR_RS03845 histidinol-phosphate phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.1   0.0   3.9e-95   3.9e-95       3     251 ..      11     258 ..       9     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 304.1 bits;  conditional E-value: 3.9e-95
                                 TIGR02067   3 alalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeed 71 
                                               +la++la+a+g +i +yfr+  ++vd k+d +pVt+ADr+aE++ir++i+a++Pddgi+GEEfg+++ d
  lcl|FitnessBrowser__azobra:AZOBR_RS03845  11 TLAERLADASGPVIRQYFRT-PVAVDDKADASPVTIADREAERTIRAIIEAERPDDGIYGEEFGTKNLD 78 
                                               6899****************.67777788888************************************* PP

                                 TIGR02067  72 aeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrvs 140
                                               ae+vWv+DPiDGTksFi+G P++gtLiaLl+ g+pvlGvi+qP++++r+++++g+ +l ng  +++rv+
  lcl|FitnessBrowser__azobra:AZOBR_RS03845  79 AEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLGVEGRPTLFNG--QPARVR 145
                                               ***********************************************************97..8***** PP

                                 TIGR02067 141 evak.lsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDia 208
                                               e+a  l++A+l ttsp +l+  ++++af++++ +a++++yggdcy+y l+A+G  dlvve++l++yD+a
  lcl|FitnessBrowser__azobra:AZOBR_RS03845 146 ECAGgLAAATLGTTSP-DLFPGADQDAFRRVAGAAKVSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFA 213
                                               **95499999999999.799************************************************* PP

                                 TIGR02067 209 alipiieeAggvitdwkGkeae..eggeavaaanaalhdevlell 251
                                               al+p++++Agg +tdw+G+++   ++g++vaa++a+ h+e+l++l
  lcl|FitnessBrowser__azobra:AZOBR_RS03845 214 ALVPVVTGAGGLMTDWDGRPLDatSSGRVVAAGDARTHRETLAAL 258
                                               *******************987779*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (260 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: 10.92
//
[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