GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Dyella japonica UNC79MFTsu3.2

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate N515DRAFT_2933 N515DRAFT_2933 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= ecocyc::PRIBFAICARPISOM-MONOMER
         (245 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2933
          Length = 242

 Score =  218 bits (555), Expect = 9e-62
 Identities = 117/241 (48%), Positives = 156/241 (64%), Gaps = 4/241 (1%)

Query: 2   IIPALDLIDGTVVRLHQGDYGKQRDYGNDPLPRLQDYAAQGAEVLHLVDLTGAKDPAKRQ 61
           +IPA+DL  G VVRL QGDYG+Q  Y  +P    + YA  GA  LH+VDL GA+  +   
Sbjct: 5   VIPAIDLRTGRVVRLRQGDYGQQTTYEFEPRELARRYAEAGAAWLHVVDLDGARSGSLDN 64

Query: 62  IPLIKTLVAGVNVPVQVGGGVRSEEDVAALLEAGVARVVVGSTAVKSQDMVKGWFERFGA 121
           + +I+ L A   + VQ GGGVRSE D+  L +AGVARVVVGS A++   +V  W  +FG 
Sbjct: 65  LQVIEAL-ARDGMQVQAGGGVRSEADLQRLFDAGVARVVVGSVAIREPALVGAWLGKFGT 123

Query: 122 DALVLALDVR-IDEQGNKQVAVSGWQENSGVSLEQLVETYLPVGLKHVLCTDISRDGTLA 180
           D L +ALD R ID  G   +  +GW E    SL++L   Y   G +H+LCTDI RDG LA
Sbjct: 124 DKLTVALDTRRID--GRWALPSAGWTELEARSLDELAPWYAARGARHLLCTDIDRDGMLA 181

Query: 181 GSNVSLYEEVCARYPQVAFQSSGGIGDIDDVAALRGTGVRGVIVGRALLEGKFTVKEAIA 240
           G N+ LY ++    P +A Q+SGG+  +DD+ A R  G +GVI+GRALLEG+FT++EA+A
Sbjct: 182 GFNLELYRDLARTAPTLAVQASGGVRSVDDIVAARAAGAQGVILGRALLEGRFTIEEALA 241

Query: 241 C 241
           C
Sbjct: 242 C 242


Lambda     K      H
   0.318    0.137    0.397 

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: 174
Number of extensions: 6
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: 245
Length of database: 242
Length adjustment: 24
Effective length of query: 221
Effective length of database: 218
Effective search space:    48178
Effective search space used:    48178
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: 46 (22.3 bits)

Align candidate N515DRAFT_2933 N515DRAFT_2933 ( 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase)
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.31946.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-74  235.6   0.0    3.1e-74  235.5   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2933  N515DRAFT_2933  1-(5-phosphoribo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2933  N515DRAFT_2933  1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.5   0.0   3.1e-74   3.1e-74       1     231 []       5     239 ..       5     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 235.5 bits;  conditional E-value: 3.1e-74
                                    TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikk 66 
                                                  +iPaiDl+ G+vvrl qGd++++t+y+ +p e+a++++e ga +lHvVDLdgA++g+ +nl+vi+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2933   5 VIPAIDLRTGRVVRLRQGDYGQQTTYEFEPRELARRYAEAGAAWLHVVDLDGARSGSLDNLQVIEA 70 
                                                  89**************************************************************** PP

                                    TIGR00007  67 iveelevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakeg 132
                                                  ++++  ++vq GGG+Rs +++++l+++gv+rv++g++a+++p+lv  +l ++g++k++v+lD+++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2933  71 LARD-GMQVQAGGGVRSEADLQRLFDAGVARVVVGSVAIREPALVGAWLGKFGTDKLTVALDTRRI 135
                                                  **76.67********************************************************987 PP

                                    TIGR00007 133 ....evavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvke.aevevi 193
                                                       +   GW+e +  sl ela  ++  g++++++Tdi++dG+l+G+n+el+++l+++  +  v+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 136 dgrwALPSAGWTELEARSLDELAPWYAARGARHLLCTDIDRDGMLAGFNLELYRDLARTaPTLAVQ 201
                                                  77778889*************************************************9999***** PP

                                    TIGR00007 194 asGGvssiedvkalkklgvkgvivGkAlyegklklkea 231
                                                  asGGv+s++d+ a++++g++gvi+G+Al+eg+++++ea
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2933 202 ASGGVRSVDDIVAARAAGAQGVILGRALLEGRFTIEEA 239
                                                  **********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (242 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 5.59
//
[ok]

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