GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisN in Dyella japonica UNC79MFTsu3.2

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate N515DRAFT_2935 N515DRAFT_2935 imidazoleglycerol-phosphate dehydratase

Query= SwissProt::Q9S5G5
         (355 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2935 N515DRAFT_2935
           imidazoleglycerol-phosphate dehydratase
          Length = 354

 Score =  387 bits (994), Expect = e-112
 Identities = 196/355 (55%), Positives = 242/355 (68%), Gaps = 1/355 (0%)

Query: 1   MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPQLLKLQKAGYKLVMITNQDGLG 60
           MS+K LF+DRDG LI EP +D Q+D ++KLA  PGVI  L +   AGY+LVM+TNQDGLG
Sbjct: 1   MSRKLLFVDRDGCLIEEP-ADEQIDSYEKLALLPGVIAALQRCVAAGYELVMVTNQDGLG 59

Query: 61  TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120
           T SFP+A F GPH L+M+I  SQGV+F EVLI    P D  D RKP + ++  YLA+   
Sbjct: 60  TDSFPEAHFTGPHELLMRILASQGVRFREVLIDRSFPRDGLDTRKPGIGMLRHYLADDGW 119

Query: 121 DRANSYVIGDRATDIQLAENMGINGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180
            RA S ++GDR TD+Q A NMG+ G     + L W  I  QL    R A V RNT+ET+I
Sbjct: 120 SRAASAMVGDRQTDLQFAANMGVRGFLVGPKGLAWEEIAHQLLDAPRTATVTRNTRETRI 179

Query: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240
            V+V LDR    K  TG+GFFDHML+QI  HGGF +E+   GD  ID+HHT+ED  LALG
Sbjct: 180 TVRVDLDRVAEPKAQTGLGFFDHMLEQIGKHGGFALELECDGDTRIDEHHTIEDCALALG 239

Query: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300
           +AL+ ALGDKRGI R+GF LPMDE  A  ALD+SGRP+  ++  F  +RVGD+ TE++ H
Sbjct: 240 QALRQALGDKRGIARYGFTLPMDESQASAALDLSGRPYFVFEGSFPRERVGDVPTELVPH 299

Query: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355
           FFRSL  T+G  LHL   G N HH VE+ FK   R LRQA+R EG  LPS+KG L
Sbjct: 300 FFRSLCETLGANLHLSVYGDNAHHMVEACFKVVARALRQALRREGSELPSTKGAL 354


Lambda     K      H
   0.322    0.140    0.420 

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: 426
Number of extensions: 16
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: 355
Length of database: 354
Length adjustment: 29
Effective length of query: 326
Effective length of database: 325
Effective search space:   105950
Effective search space used:   105950
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate N515DRAFT_2935 N515DRAFT_2935 (imidazoleglycerol-phosphate dehydratase)
to HMM TIGR01261 (hisB: 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/TIGR01261.hmm
# target sequence database:        /tmp/gapView.21427.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01261  [M=161]
Accession:   TIGR01261
Description: hisB_Nterm: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    8.4e-63  196.8   0.0    1.2e-62  196.3   0.0    1.2  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2935  N515DRAFT_2935 imidazoleglycerol


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2935  N515DRAFT_2935 imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.3   0.0   1.2e-62   1.2e-62       2     160 ..       4     161 ..       3     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 196.3 bits;  conditional E-value: 1.2e-62
                                    TIGR01261   2 kilfidrdGtlieePksdfqvdaleklklekkvipallklkeagyklvlvtnqdGlGtesfPkedf 67 
                                                  k+lf+drdG lieeP  d q+d++ekl+l ++vi+al +  +agy+lv+vtnqdGlGt+sfP+++f
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2935   4 KLLFVDRDGCLIEEPA-DEQIDSYEKLALLPGVIAALQRCVAAGYELVMVTNQDGLGTDSFPEAHF 68 
                                                  89*************9.99*********************************************** PP

                                    TIGR01261  68 dkphalmlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdl 133
                                                   +ph+l++ i+ s+G+ f++vli+++f+ d  ++rkP i++l++yl+++   ++ s+++Gdr+tdl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2935  69 TGPHELLMRILASQGVRFREVLIDRSFPRDGLDTRKPGIGMLRHYLADDGWSRAASAMVGDRQTDL 134
                                                  ****************************************************************** PP

                                    TIGR01261 134 qlaenlgirglkykeeelnwkeiakel 160
                                                  q+a n+g+rg+    + l+w+eia++l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2935 135 QFAANMGVRGFLVGPKGLAWEEIAHQL 161
                                                  *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (161 nodes)
Target sequences:                          1  (354 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: 11.22
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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