GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Sphingomonas koreensis DSMZ 15582

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate Ga0059261_2035 Ga0059261_2035 histidinol-phosphatase, inositol monophosphatase family

Query= reanno::Korea:Ga0059261_2035
         (260 letters)



>FitnessBrowser__Korea:Ga0059261_2035
          Length = 260

 Score =  523 bits (1347), Expect = e-153
 Identities = 260/260 (100%), Positives = 260/260 (100%)

Query: 1   MPVSQADIDLAGRLADAAGAAIRPYFRAEHGLESKDDSSPVTLADKAAEAAMRRLIIAER 60
           MPVSQADIDLAGRLADAAGAAIRPYFRAEHGLESKDDSSPVTLADKAAEAAMRRLIIAER
Sbjct: 1   MPVSQADIDLAGRLADAAGAAIRPYFRAEHGLESKDDSSPVTLADKAAEAAMRRLIIAER 60

Query: 61  PMDAIIGEEEDDRPGTSGRIWVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPI 120
           PMDAIIGEEEDDRPGTSGRIWVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPI
Sbjct: 61  PMDAIIGEEEDDRPGTSGRIWVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPI 120

Query: 121 IKERWLGVTGRETLFNGKPARARTCRELSKALLATTSPALFTDGQLHAFEHVDAAVMSTV 180
           IKERWLGVTGRETLFNGKPARARTCRELSKALLATTSPALFTDGQLHAFEHVDAAVMSTV
Sbjct: 121 IKERWLGVTGRETLFNGKPARARTCRELSKALLATTSPALFTDGQLHAFEHVDAAVMSTV 180

Query: 181 LGGDCYNYGLVASGHLDIVIEAGLKLHDFAALVPVVEGAGGRMCDWQGDPLHAGSNGEVI 240
           LGGDCYNYGLVASGHLDIVIEAGLKLHDFAALVPVVEGAGGRMCDWQGDPLHAGSNGEVI
Sbjct: 181 LGGDCYNYGLVASGHLDIVIEAGLKLHDFAALVPVVEGAGGRMCDWQGDPLHAGSNGEVI 240

Query: 241 AAGDPARIEELVEALACQGH 260
           AAGDPARIEELVEALACQGH
Sbjct: 241 AAGDPARIEELVEALACQGH 260


Lambda     K      H
   0.320    0.138    0.419 

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: 404
Number of extensions: 8
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 Ga0059261_2035 Ga0059261_2035 (histidinol-phosphatase, inositol monophosphatase family)
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.25888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.9e-90  287.4   0.0    5.7e-90  287.2   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2035  Ga0059261_2035 histidinol-phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2035  Ga0059261_2035 histidinol-phosphatase, inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.2   0.0   5.7e-90   5.7e-90       3     251 ..       9     255 ..       7     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 287.2 bits;  conditional E-value: 5.7e-90
                                 TIGR02067   3 alalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeed 71 
                                                la +la+aag+ai +yfra++   ++k+d++pVt AD+aaE+a+r+li a++P d+i+GEE +++ ++
  lcl|FitnessBrowser__Korea:Ga0059261_2035   9 DLAGRLADAAGAAIRPYFRAEH-GLESKDDSSPVTLADKAAEAAMRRLIIAERPMDAIIGEEEDDRPGT 76 
                                               57899***************66.566677778************************************* PP

                                 TIGR02067  72 aeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrvs 140
                                               +++ WvlDPiDGT+sFi G P++gtLiaLle+g pvlG+i+qP+++er+++++g+++l ng  +++r++
  lcl|FitnessBrowser__Korea:Ga0059261_2035  77 SGRIWVLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPIIKERWLGVTGRETLFNG--KPARAR 143
                                               ***********************************************************98..8***** PP

                                 TIGR02067 141 evaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaa 209
                                               ++ +ls+A+l+ttsp al++ ++ +afe++ +++  t++ggdcy+y lvAsG+ d+v+ea+l+++D+aa
  lcl|FitnessBrowser__Korea:Ga0059261_2035 144 TCRELSKALLATTSP-ALFTDGQLHAFEHVDAAVMSTVLGGDCYNYGLVASGHLDIVIEAGLKLHDFAA 211
                                               ***************.89999************************************************ PP

                                 TIGR02067 210 lipiieeAggvitdwkGkeae..eggeavaaanaalhdevlell 251
                                               l+p++e+Agg + dw+G +++  ++ge++aa+++a  +e++e+l
  lcl|FitnessBrowser__Korea:Ga0059261_2035 212 LVPVVEGAGGRMCDWQGDPLHagSNGEVIAAGDPARIEELVEAL 255
                                               *******************997778999******9999999887 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.98
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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