Alignments for a candidate for hisG in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Pedobacter sp. GW460-11-11-14-LB5

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate CA265_RS03640 CA265_RS03640 ATP phosphoribosyltransferase

Query= BRENDA::Q5HSJ4
         (299 letters)



>FitnessBrowser__Pedo557:CA265_RS03640
          Length = 283

 Score =  233 bits (594), Expect = 4e-66
 Identities = 123/293 (41%), Positives = 189/293 (64%), Gaps = 13/293 (4%)

Query: 7   LRIAIQKSGRLSKESIELLSECGVKMHIHEQSLIAFSTNLPIDILRVRDDDIPGLIFDGV 66
           L+IAIQKSGRL+++S+E+L  CG+    ++ SLI+  TN P++IL +RDDDIP  + DG+
Sbjct: 4   LKIAIQKSGRLNEKSVEILKNCGLSFENYKSSLISTVTNFPLEILFLRDDDIPEYVQDGI 63

Query: 67  VDLGIIGENVLEENELERQSLGENPSYKLLKKLDFGYCRLSLALPQENKFQNLKDFEGLR 126
            DLGI+GENV+ E + E            L+KL FG C L +A+   +  Q L++  G  
Sbjct: 64  ADLGIVGENVIVETKAE---------VDYLQKLGFGKCTLKIAVQATSNIQKLEELNGKA 114

Query: 127 IATSYPQLLKRFMKENGINYKNCTLTGSVEVAPRANLADAICDLVSSGATLQANNLKEVK 186
           IATSYP +L++F++E GI     T++GSVE+ P   L+DAI D+VS+G TL++N LK   
Sbjct: 115 IATSYPVILEKFLQEKGIKSDIRTISGSVEIGPGLGLSDAIFDIVSTGGTLKSNGLKPFA 174

Query: 187 VIYESRACLIQKENALSKEKQALVDKIMLRVAGVMQARESKYIMLHAPKEKLDKIQALLP 246
            + +S A LI  ++     +   V +++ R+  V+ A+ +KY++L+  K+ L K+  LLP
Sbjct: 175 DVMQSEAVLIGNKSIADNPE---VAELLQRIRSVLSAKSNKYVVLNVSKDNLQKVVDLLP 231

Query: 247 GVERPTILPLAHDEKNVALHMVSKENLFWETMEALKEEGASSILVLPIEKMLK 299
           GV+ PT++PL  +   VA+H V  E  FW+ + +LK  GA  ILV+PIEK+++
Sbjct: 232 GVKSPTVVPL-FEPNWVAVHSVIAEEDFWDKINSLKAAGAEGILVMPIEKIIR 283


Lambda     K      H
   0.317    0.135    0.371 

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: 233
Number of extensions: 12
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: 299
Length of database: 283
Length adjustment: 26
Effective length of query: 273
Effective length of database: 257
Effective search space:    70161
Effective search space used:    70161
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate CA265_RS03640 CA265_RS03640 (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.11330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    1.3e-60  190.5   0.1    2.1e-60  189.8   0.1    1.3  1  lcl|FitnessBrowser__Pedo557:CA265_RS03640  CA265_RS03640 ATP phosphoribosyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS03640  CA265_RS03640 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   0.1   2.1e-60   2.1e-60       1     182 [.       4     184 ..       4     185 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 2.1e-60
                                  TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitG 67 
                                                l+iA++  Grl e+++++l+++gl++++ +  +li ++++ ++e+l+lr++dip+yv++g+adlGi+G
  lcl|FitnessBrowser__Pedo557:CA265_RS03640   4 LKIAIQkSGRLNEKSVEILKNCGLSFENYK-SSLISTVTNFPLEILFLRDDDIPEYVQDGIADLGIVG 70 
                                                89****99********************99.99*********************************** PP

                                  TIGR00070  68 kDlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveiv 135
                                                ++++ E +a+v  l +lgfgkc+l +Av+ +s++++le+l+ gk iAT+yp + +++l++kg+k +i 
  lcl|FitnessBrowser__Pedo557:CA265_RS03640  71 ENVIVETKAEVDYLQKLGFGKCTLKIAVQATSNIQKLEELN-GKAIATSYPVILEKFLQEKGIKSDIR 137
                                                *****************************************.9************************* PP

                                  TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarli 182
                                                 ++G+vE+ p lgl+daI+Div+tG tL++ngLk ++++++s+a+li
  lcl|FitnessBrowser__Pedo557:CA265_RS03640 138 TISGSVEIGPGLGLSDAIFDIVSTGGTLKSNGLKPFADVMQSEAVLI 184
                                                **********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (283 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: 8.14
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis