GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Sphingomonas indica Dd16

Align ATP phosphoribosyltransferase (characterized)
to candidate WP_085217032.1 B9N75_RS00535 ATP phosphoribosyltransferase

Query= CharProtDB::CH_024688
         (299 letters)



>NCBI__GCF_900177405.1:WP_085217032.1
          Length = 296

 Score =  291 bits (744), Expect = 2e-83
 Identities = 154/297 (51%), Positives = 202/297 (68%), Gaps = 4/297 (1%)

Query: 2   TDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPGL 61
           TD++RL IA+QKSGRL++ SR LL   G+++      L A  EN P D++ VRDDDIP  
Sbjct: 3   TDDSRLHIAIQKSGRLAEQSRRLLRDAGLRLQEGKNALTARIENFPADLMYVRDDDIPTF 62

Query: 62  VMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPLS 121
           V DGV +LGI+G NVL E  L  R    D RY  L  L FG C L LA      W G   
Sbjct: 63  VADGVCELGIVGSNVLREFELAER----DSRYEILSPLGFGRCALKLAAAATSDWHGLAD 118

Query: 122 LNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEANG 181
           L   RIATSYPH+++ +L+Q+ I+     +NG+VE+APR G+A  ICDLVSTGATLEANG
Sbjct: 119 LGEARIATSYPHIVRDFLEQRQIAATVVTMNGAVELAPRLGIAPFICDLVSTGATLEANG 178

Query: 182 LREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDEV 241
           LR +E ++ S+A L++  G ++E++Q+ ++ L+ RI GV+  +ESKYIM++AP   L  +
Sbjct: 179 LRPLETLFESEAVLVRTRGALDEARQETMNGLVRRIGGVLATKESKYIMLNAPEAALPAI 238

Query: 242 IALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMM 298
            ALLPGAE PTILPL     + A+H V  E++FWET+ KLKA GAS+ILVLPIEKMM
Sbjct: 239 SALLPGAEAPTILPLHARPGQFAVHAVCQESVFWETLHKLKANGASAILVLPIEKMM 295


Lambda     K      H
   0.320    0.137    0.389 

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: 272
Number of extensions: 9
Number of successful extensions: 2
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: 299
Length of database: 296
Length adjustment: 26
Effective length of query: 273
Effective length of database: 270
Effective search space:    73710
Effective search space used:    73710
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: 48 (23.1 bits)

Align candidate WP_085217032.1 B9N75_RS00535 (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.69534.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.5e-57  180.5   0.0    1.9e-57  180.1   0.0    1.1  1  NCBI__GCF_900177405.1:WP_085217032.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217032.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   0.0   1.9e-57   1.9e-57       1     182 [.       8     193 ..       8     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 1.9e-57
                             TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlle 72 
                                           l+iA++  Grl+e++ +ll++agl+l++ +  +l+a++e+ + +++++r++dipt+v++g+ +lGi+G+++l+
  NCBI__GCF_900177405.1:WP_085217032.1   8 LHIAIQkSGRLAEQSRRLLRDAGLRLQEGK-NALTARIENFPADLMYVRDDDIPTFVADGVCELGIVGSNVLR 79 
                                           78****99*******************999.9***************************************** PP

                             TIGR00070  73 E.....seadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGa 140
                                           E     +++ ++ l  lgfg+c l lA+  +sd++ l+dl  ++riAT+yp+++r++le++++ +++v ++Ga
  NCBI__GCF_900177405.1:WP_085217032.1  80 EfelaeRDSRYEILSPLGFGRCALKLAAAATSDWHGLADLG-EARIATSYPHIVRDFLEQRQIAATVVTMNGA 151
                                           *87754455599999**************************.79***************************** PP

                             TIGR00070 141 vElapllgladaIvDivetGttLrengLkiieeilessarli 182
                                           vElap+lg+a +I+D+v+tG+tL++ngL+ +e+++es+a+l+
  NCBI__GCF_900177405.1:WP_085217032.1 152 VELAPRLGIAPFICDLVSTGATLEANGLRPLETLFESEAVLV 193
                                           ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (296 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: 13.97
//
[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