GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisA in Desulfovibrio vulgaris Miyazaki F

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate 8502414 DvMF_3120 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)

Query= BRENDA::P16250
         (240 letters)



>lcl|FitnessBrowser__Miya:8502414 DvMF_3120
           1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase (RefSeq)
          Length = 243

 Score =  168 bits (426), Expect = 8e-47
 Identities = 96/236 (40%), Positives = 136/236 (57%), Gaps = 4/236 (1%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           L PAVD++DG+ VRL  G +  ET +   P   A  WQ  GA+WLH++DLD AF G   N
Sbjct: 3   LFPAVDIKDGRCVRLRQGRADAETVFSDDPAAMARHWQDQGAKWLHVIDLDGAFSGMPAN 62

Query: 64  RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123
             LI  +   + + V+L GGIRD+ T  A L  G  R+ +GT ALE P+  A++ A    
Sbjct: 63  FELIRRICADLSVPVQLGGGIRDEATAKAYLDAGVERLIIGTVALEEPDLYARLCATFPG 122

Query: 124 KIAVGLDVRGTTLRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLELL 182
           +I V LD  G  L+ +GW  D G  + + L RL   G A  + TDI +DG   G NL  L
Sbjct: 123 RIGVSLDAEGGRLKTKGWVADSGLTVDDVLPRLLAAGTAFVIYTDIDRDGMQTGVNLSAL 182

Query: 183 KNVCAATDRPVVASGGVSSLDDLRAIAGL-VPAGVEGAIVGKALYAKAFTLEEALE 237
           + +      PV+A+GGV++L+D+RA+  + + + VEGAI G+A+Y     L  A+E
Sbjct: 183 ERLAGMCPVPVIAAGGVATLEDVRALYPMTLTSSVEGAITGRAIYTGTLDLHAAME 238


Lambda     K      H
   0.315    0.133    0.385 

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: 181
Number of extensions: 16
Number of successful extensions: 6
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: 240
Length of database: 243
Length adjustment: 23
Effective length of query: 217
Effective length of database: 220
Effective search space:    47740
Effective search space used:    47740
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

Align candidate 8502414 DvMF_3120 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq))
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))

# 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/TIGR00007.hmm
# target sequence database:        /tmp/gapView.16830.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00007  [M=231]
Accession:   TIGR00007
Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.8e-78  248.7   0.0    3.2e-78  248.5   0.0    1.0  1  lcl|FitnessBrowser__Miya:8502414  DvMF_3120 1-(5-phosphoribosyl)-5


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8502414  DvMF_3120 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazo
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.5   0.0   3.2e-78   3.2e-78       2     230 ..       4     235 ..       3     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 248.5 bits;  conditional E-value: 3.2e-78
                         TIGR00007   2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqvG 78 
                                       +Pa+D+k+G++vrl qG+ d +tv+sddp+++a++++++ga++lHv+DLdgA++g + n+e+i++i+ +l+v+vq+G
  lcl|FitnessBrowser__Miya:8502414   4 FPAVDIKDGRCVRLRQGRADAETVFSDDPAAMARHWQDQGAKWLHVIDLDGAFSGMPANFELIRRICADLSVPVQLG 80 
                                       8**************************************************************************** PP

                         TIGR00007  79 GGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslvelakkle 155
                                       GGiR+ ++++++l++gver+iigt+a+e+p+l ++l +++   +i vslDa++g++++kGW ++s l++ +++ +l 
  lcl|FitnessBrowser__Miya:8502414  81 GGIRDEATAKAYLDAGVERLIIGTVALEEPDLYARLCATFP-GRIGVSLDAEGGRLKTKGWVADSGLTVDDVLPRLL 156
                                       ****************************************9.*********************************** PP

                         TIGR00007 156 elgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk....lgvkgvivGkAlyegklkl 228
                                        +g++ +i+Tdi++dG+ +Gvn++++++l+    v+via+GGv++ edv+al+     + v+g+i G+A+y+g+l+l
  lcl|FitnessBrowser__Miya:8502414 157 AAGTAFVIYTDIDRDGMQTGVNLSALERLAGMCPVPVIAAGGVATLEDVRALYPmtltSSVEGAITGRAIYTGTLDL 233
                                       ****************************************************987777889**************98 PP

                         TIGR00007 229 ke 230
                                       ++
  lcl|FitnessBrowser__Miya:8502414 234 HA 235
                                       76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (243 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: 6.65
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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