GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Caldicellulosiruptor kronotskyensis 2002

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_013430203.1 CALKRO_RS06250 ATP phosphoribosyltransferase

Query= reanno::WCS417:GFF870
         (211 letters)



>NCBI__GCF_000166775.1:WP_013430203.1
          Length = 209

 Score =  181 bits (458), Expect = 1e-50
 Identities = 102/210 (48%), Positives = 144/210 (68%), Gaps = 6/210 (2%)

Query: 1   MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE 60
           M+TIAL KGR+   T+ LL  A +V  +  ++SRKLII  TQ+ +R L+V+  DVPTYVE
Sbjct: 1   MITIALPKGRLAQQTVELLKRASLVDIDISEESRKLIIEDTQNSLRFLMVKPFDVPTYVE 60

Query: 61  HGAADLGVAGKDVLMEYGGQGLYEPLDLRIALCKLMTAGRVGDVE---PKGRLRVATKFV 117
           +G AD+GV GKDVL+E   + +YE LDL+I  C +  AG  G  E    K    +ATKF 
Sbjct: 61  YGVADVGVVGKDVLLEM-NKRVYELLDLKIGKCFVALAGPKGISEALLKKPDKTIATKFP 119

Query: 118 NVAKRYYAE-QGRQVDIIKLYGSMELAPLIGLADKIIDVVDTGNTLRANGLEPQEFIADI 176
           N+AK Y+   +G  V IIKL GS+ELAP++GL+D I+D+V++G TL+ NGLE  E + DI
Sbjct: 120 NIAKEYFENVRGEDVKIIKLNGSVELAPILGLSDMIVDIVESGRTLKENGLEVYEKLYDI 179

Query: 177 SSRLIVNKASMKMQHARIQALIDTLRKAVE 206
           S+RLI N+AS+K++  +I  +I+ L + +E
Sbjct: 180 SARLIANRASLKLK-TQIDDIINRLERMIE 208


Lambda     K      H
   0.320    0.138    0.384 

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: 160
Number of extensions: 4
Number of successful extensions: 4
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: 211
Length of database: 209
Length adjustment: 21
Effective length of query: 190
Effective length of database: 188
Effective search space:    35720
Effective search space used:    35720
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: 45 (21.9 bits)

Align candidate WP_013430203.1 CALKRO_RS06250 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))

# 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/TIGR00070.hmm
# target sequence database:        /tmp/gapView.2178506.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00070  [M=183]
Accession:   TIGR00070
Description: hisG: ATP phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    5.9e-66  207.9   0.1    6.8e-66  207.7   0.1    1.0  1  NCBI__GCF_000166775.1:WP_013430203.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430203.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.7   0.1   6.8e-66   6.8e-66       1     183 []       2     185 ..       2     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 207.7 bits;  conditional E-value: 6.8e-66
                             TIGR00070   1 lriAlpKGrleeetlklleka...glklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDl 70 
                                           ++iAlpKGrl+++t++ll++a   ++++s+++ rkli++++++ +++l++++ d+ptyve+g+ad+G++GkD+
  NCBI__GCF_000166775.1:WP_013430203.1   2 ITIALPKGRLAQQTVELLKRAslvDIDISEES-RKLIIEDTQNSLRFLMVKPFDVPTYVEYGVADVGVVGKDV 73 
                                           79*******************87788888888.**************************************** PP

                             TIGR00070  71 leEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkg.vkveivkleGavE 142
                                           l E ++ v+elldl++gkc ++lA p+  +   l+  k++k iATk+pn+++ey+e+ +  +v+i+kl+G+vE
  NCBI__GCF_000166775.1:WP_013430203.1  74 LLEMNKRVYELLDLKIGKCFVALAGPKGISEALLK--KPDKTIATKFPNIAKEYFENVRgEDVKIIKLNGSVE 144
                                           ****************************9444422..3379***************97769************ PP

                             TIGR00070 143 lapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                           lap+lgl+d+IvDive+G+tL+engL+++e+++++sarlia
  NCBI__GCF_000166775.1:WP_013430203.1 145 LAPILGLSDMIVDIVESGRTLKENGLEVYEKLYDISARLIA 185
                                           ***************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (209 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: 11.12
//
[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