GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Xenophilus azovorans DSM 13620

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_038217853.1 Q392_RS29640 histidinol-phosphatase

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



>NCBI__GCF_000745855.1:WP_038217853.1
          Length = 258

 Score =  244 bits (624), Expect = 1e-69
 Identities = 128/255 (50%), Positives = 164/255 (64%), Gaps = 2/255 (0%)

Query: 4   PCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEAERP 63
           P   PL+  A  LADA+      YFR P+ +  KAD SPVT+ADR AE+ +R ++ A+ P
Sbjct: 3   PAIHPLLATAHALADAAARQSMAYFRQPLEIVTKADDSPVTLADRAAEQAMRDVLAAQAP 62

Query: 64  DDGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIV 123
           +DGIYGEE G + LDA  VWV+DPIDGT+SFITG P++GTLIA    GR  LG+ID P++
Sbjct: 63  EDGIYGEEHGQQRLDAGRVWVLDPIDGTRSFITGSPLWGTLIAAFSGGRVELGMIDMPVL 122

Query: 124 RDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSV 183
            +RW+G +G   + NGQP RVR C   LA A + TTSPD+F  AD   F  ++    +  
Sbjct: 123 GERWIGQDG-VAMRNGQPVRVRGCT-RLAEARIVTTSPDIFAPADWAVFDALSRRCAMRR 180

Query: 184 YGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVV 243
           +GGDCY Y  LA G  DLVVE+GL+ YD+     V+  AGG++TDW+GRPL      RVV
Sbjct: 181 FGGDCYGYAQLAGGTIDLVVETGLQPYDYLGPAGVIEAAGGVITDWEGRPLGLQPDCRVV 240

Query: 244 AAGDARTHRETLAAL 258
           AA     HR  LA L
Sbjct: 241 AAATPELHRAALAVL 255


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: 280
Number of extensions: 13
Number of successful extensions: 3
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: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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 WP_038217853.1 Q392_RS29640 (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.4004837.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.9e-88  281.2   0.1    4.4e-88  281.0   0.1    1.0  1  NCBI__GCF_000745855.1:WP_038217853.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038217853.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.0   0.1   4.4e-88   4.4e-88       2     252 .]       9     256 ..       8     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 281.0 bits;  conditional E-value: 4.4e-88
                             TIGR02067   2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeedaey 74 
                                           la a++la+aa+++ + yfr+  ++v k +d+ pVt ADraaE+a+r+++aa+ P+dgi+GEE+g+++ da++
  NCBI__GCF_000745855.1:WP_038217853.1   9 LATAHALADAAARQSMAYFRQPLEIVTKADDS-PVTLADRAAEQAMRDVLAAQAPEDGIYGEEHGQQRLDAGR 80 
                                           57899****************88887776666.**************************************** PP

                             TIGR02067  75 vWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrvsevaklsd 147
                                           vWvlDPiDGT+sFi+G P+wgtLia  ++g++ lG+i++P+lger++++ g ++      +++rv+ +++l++
  NCBI__GCF_000745855.1:WP_038217853.1  81 VWVLDPIDGTRSFITGSPLWGTLIAAFSGGRVELGMIDMPVLGERWIGQDGVAMRNG---QPVRVRGCTRLAE 150
                                           ************************************************999887664...7************ PP

                             TIGR02067 148 AvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiieeAggv 220
                                           A +vttsp +++++++ + f++l r++ + r+ggdcy+ya +A G++dlvve++l+pyD+   + +ie Aggv
  NCBI__GCF_000745855.1:WP_038217853.1 151 ARIVTTSP-DIFAPADWAVFDALSRRCAMRRFGGDCYGYAQLAGGTIDLVVETGLQPYDYLGPAGVIEAAGGV 222
                                           ********.799************************************************************* PP

                             TIGR02067 221 itdwkGkeae..eggeavaaanaalhdevlellk 252
                                           itdw+G+++    + ++vaaa+++lh+++l++l+
  NCBI__GCF_000745855.1:WP_038217853.1 223 ITDWEGRPLGlqPDCRVVAAATPELHRAALAVLQ 256
                                           ********9776899***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (258 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: 19.07
//
[ok]

This GapMind analysis is from Jul 25 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