GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Streptacidiphilus oryzae TH49

Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate WP_037573048.1 BS73_RS15920 histidinol-phosphatase

Query= SwissProt::Q9K4B1
         (266 letters)



>NCBI__GCF_000744815.1:WP_037573048.1
          Length = 264

 Score =  400 bits (1028), Expect = e-116
 Identities = 196/263 (74%), Positives = 221/263 (84%)

Query: 1   MPDYLDDLRLAHVLADAADAATMDRFKALDLKVETKPDMTPVSEADKAAEELIRGHLSRA 60
           MPD+ DDLRLAHVLAD AD+ T +RFKALDL+VETKPD+TPVS+ADKAAE+++R  LSRA
Sbjct: 1   MPDFHDDLRLAHVLADHADSVTTERFKALDLRVETKPDLTPVSDADKAAEDVVRSVLSRA 60

Query: 61  RPRDSVHGEEFGVAGTGPRRWVIDPIDGTKNYVRGVPVWATLIALMEAKEGGYQPVVGLV 120
           RPRD+V GEE GV G GPRRWVIDPIDGTKNYVRGVPVWATLI+L+E   GG +PVVGLV
Sbjct: 61  RPRDAVMGEEHGVTGHGPRRWVIDPIDGTKNYVRGVPVWATLISLLELGPGGEEPVVGLV 120

Query: 121 SAPALGRRWWAVEDHGAFTGRSLTSAHRLHVSQVSTLSDASFAYSSLSGWEEQGRLDGFL 180
           SAPALG+RWW+ +  GAFTGRSL  A RL VS VS LSDAS +YSSL+GWEE+G L  F+
Sbjct: 121 SAPALGKRWWSAKGSGAFTGRSLARATRLQVSDVSRLSDASLSYSSLTGWEERGLLPNFV 180

Query: 181 DLTREVWRTRAYGDFWPYMMVAEGSVDLCAEPELSLWDMAANAIIVTEAGGTFTGLDGRP 240
           DL+R+VWRTRA+GDFW YMMVAEG+VDL AEPELSLWDMAA   IVTEAGG FT L GRP
Sbjct: 181 DLSRKVWRTRAFGDFWSYMMVAEGAVDLAAEPELSLWDMAAPCAIVTEAGGRFTDLQGRP 240

Query: 241 GPHSGNAAASNGRLHDELLGYLN 263
           G H  NA ASNG LH+ LLG LN
Sbjct: 241 GVHGPNAVASNGLLHEALLGSLN 263


Lambda     K      H
   0.318    0.135    0.418 

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: 297
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: 266
Length of database: 264
Length adjustment: 25
Effective length of query: 241
Effective length of database: 239
Effective search space:    57599
Effective search space used:    57599
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_037573048.1 BS73_RS15920 (histidinol-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.4059402.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    5.1e-88  280.8   0.0    5.8e-88  280.6   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037573048.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037573048.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.6   0.0   5.8e-88   5.8e-88       2     251 ..       8     262 ..       7     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 280.6 bits;  conditional E-value: 5.8e-88
                             TIGR02067   2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeedaey 74 
                                           l+la+ la+ a+++++++f+a dl v++k+d tpV++AD+aaE+++r+++++++P+d+++GEE+g  +++  +
  NCBI__GCF_000744815.1:WP_037573048.1   8 LRLAHVLADHADSVTTERFKALDLRVETKPDLTPVSDADKAAEDVVRSVLSRARPRDAVMGEEHGV-TGHGPR 79 
                                           6899*************************************************************5.78889* PP

                             TIGR02067  75 vWvlDPiDGTksFirGvPvwgtLiaLlekgk....pvlGvisqPalgerfvaakgegallngge...relrvs 140
                                           +Wv+DPiDGTk+++rGvPvw+tLi+Lle g     pv+G++s+Palg+r+++akg+ga++ ++     +l+vs
  NCBI__GCF_000744815.1:WP_037573048.1  80 RWVIDPIDGTKNYVRGVPVWATLISLLELGPggeePVVGLVSAPALGKRWWSAKGSGAFTGRSLaraTRLQVS 152
                                           ***************************96544445*************************87335789***** PP

                             TIGR02067 141 evaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipi 213
                                            v++lsdA+l+++s + +e+++   +f +l rk+++tr++gd+++y++vA+G+vdl++e+els++D+aa   i
  NCBI__GCF_000744815.1:WP_037573048.1 153 DVSRLSDASLSYSSLTGWEERGLLPNFVDLSRKVWRTRAFGDFWSYMMVAEGAVDLAAEPELSLWDMAAPCAI 225
                                           ************************************************************************* PP

                             TIGR02067 214 ieeAggvitdwkGkeaeeggeavaaanaalhdevlell 251
                                           ++eAgg +td++G++  +g +a +a+n  lh+++l +l
  NCBI__GCF_000744815.1:WP_037573048.1 226 VTEAGGRFTDLQGRPGVHGPNA-VASNGLLHEALLGSL 262
                                           **********************.999*******99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (264 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: 12.89
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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