GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argC in Dechlorosoma suillum PS

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate Dsui_0782 Dsui_0782 N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form

Query= curated2:Q8Y339
         (337 letters)



>lcl|FitnessBrowser__PS:Dsui_0782 Dsui_0782
           N-acetyl-gamma-glutamyl-phosphate reductase, uncommon
           form
          Length = 319

 Score =  382 bits (980), Expect = e-111
 Identities = 185/319 (57%), Positives = 243/319 (76%), Gaps = 4/319 (1%)

Query: 1   MAFKVFVDGQEGTTGLRLLDYLSQRDDIELLRIAEDRRKDPAERAKFLNAADVAFLCLPD 60
           M FKVF+DG+ GTTGL++ + LS R +IE+L I ED+RKDPA +A+++N+ADV FLCLPD
Sbjct: 1   MTFKVFIDGRHGTTGLKIDERLSIRPEIEILTIPEDKRKDPAVKAEYINSADVVFLCLPD 60

Query: 61  VASREAVSLV--DNPNTCIIDASTAFRTSDDWAYGLPELAPGQRERLRNSKRIAVPGCHA 118
            ASRE+V+L+   N  T  +DASTA RT+ DW YGLPEL  GQRER+  ++++AVPGCHA
Sbjct: 61  AASRESVALLAPGNTRTRFLDASTAHRTNPDWVYGLPELNGGQRERVAKAQKVAVPGCHA 120

Query: 119 SAFVLLMRPLVEAGIVPADYPITAFSLTGYSGGGKKMIADYL--AADNPKLQSPRPYALA 176
           S F++LM PLV  GIVP DYP++ +S+TGYSGGGK+MIA Y   A+    ++SPR YAL 
Sbjct: 121 SGFIMLMAPLVAGGIVPKDYPVSTYSITGYSGGGKEMIASYEEPASLPDAMKSPRFYALG 180

Query: 177 LTHKHLPEMRVQSKLALPPIFTPVVGNFLKGLAVTIGLHPQHLASKVSPADIAKVFADYY 236
           LTHKHLPEM++Q+ LA  P+FTP+VGNF +G+ V + L P+ L  KV+PAD+   +++YY
Sbjct: 181 LTHKHLPEMQMQTGLAHQPLFTPIVGNFAQGMVVAVPLLPRMLGKKVTPADLQAFYSEYY 240

Query: 237 QGEQFIRVAPADNVETLDNGFFDVQGANDTNRADLFVFGSDERMVVTARLDNLGKGAAGA 296
            GE F++V P D    LDNGF      NDTNRA++FVFG  E+++V +R DNLGKGA+GA
Sbjct: 241 AGEVFVKVMPLDAAPVLDNGFLPATACNDTNRAEIFVFGHGEQILVASRFDNLGKGASGA 300

Query: 297 AVQCMNVHLGVDEATSLHV 315
           A+QCMN+ LGVDEAT L V
Sbjct: 301 AIQCMNLMLGVDEATGLAV 319


Lambda     K      H
   0.320    0.136    0.401 

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: 363
Number of extensions: 12
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: 337
Length of database: 319
Length adjustment: 28
Effective length of query: 309
Effective length of database: 291
Effective search space:    89919
Effective search space used:    89919
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: 49 (23.5 bits)

Align candidate Dsui_0782 Dsui_0782 (N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form)
to HMM TIGR01851 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))

# 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/TIGR01851.hmm
# target sequence database:        /tmp/gapView.8497.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01851  [M=310]
Accession:   TIGR01851
Description: argC_other: N-acetyl-gamma-glutamyl-phosphate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.5e-134  431.5   0.0   1.1e-133  431.3   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0782  Dsui_0782 N-acetyl-gamma-glutamy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0782  Dsui_0782 N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.3   0.0  1.1e-133  1.1e-133       2     310 .]       3     311 ..       2     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 431.3 bits;  conditional E-value: 1.1e-133
                         TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd..npntki 76 
                                       +kvfidG+ GttGl+i erl+ r ++e+l+i edkrkd++ +a+ +n+adv++lclpd a+re+v+l    n++t+ 
  lcl|FitnessBrowser__PS:Dsui_0782   3 FKVFIDGRHGTTGLKIDERLSIRPEIEILTIPEDKRKDPAVKAEYINSADVVFLCLPDAASRESVALLApgNTRTRF 79 
                                       8******************************************************************974477789* PP

                         TIGR01851  77 ldastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinavsGysGGGka 153
                                       ldasta+rt++dwvyG+pel+ +qre++a+a++va+PGc+a+g+i+l++Plv+ Gi+P d+Pv++ +++GysGGGk+
  lcl|FitnessBrowser__PS:Dsui_0782  80 LDASTAHRTNPDWVYGLPELNGGQRERVAKAQKVAVPGCHASGFIMLMAPLVAGGIVPKDYPVSTYSITGYSGGGKE 156
                                       ***************************************************************************** PP

                         TIGR01851 154 liakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhlaeldskvsaedih 230
                                       +ia+yee ++ + + ++++ y+l l+hkhlpem+ ++gla++P+ftP vG+faqG++v +pl +  l++kv+++d++
  lcl|FitnessBrowser__PS:Dsui_0782 157 MIASYEEPASLPDAMKSPRFYALGLTHKHLPEMQMQTGLAHQPLFTPIVGNFAQGMVVAVPLLPRMLGKKVTPADLQ 233
                                       ***************************************************************************** PP

                         TIGR01851 231 kalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnia 307
                                       +   eyy+Ge fvkv++ld a++ld+++l a++ n+tnr+e+fvfg    e++l+++r+dnlGkGasGaa+q++n++
  lcl|FitnessBrowser__PS:Dsui_0782 234 AFYSEYYAGEVFVKVMPLDAAPVLDNGFLPATACNDTNRAEIFVFGHG--EQILVASRFDNLGKGASGAAIQCMNLM 308
                                       **********************************************76..*************************** PP

                         TIGR01851 308 lGl 310
                                       lG+
  lcl|FitnessBrowser__PS:Dsui_0782 309 LGV 311
                                       **7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (319 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: 00:00:00.00
# Mc/sec: 9.96
//
[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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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