Alignments for a candidate for hisN in Azospirillum brasilense Sp245

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.8059.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.48
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis