GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Paraburkholderia bryophila 376MFSha3.1

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate H281DRAFT_02654 H281DRAFT_02654 N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Smeli:SMc01801
         (310 letters)



>FitnessBrowser__Burk376:H281DRAFT_02654
          Length = 309

 Score =  313 bits (801), Expect = 4e-90
 Identities = 161/308 (52%), Positives = 209/308 (67%), Gaps = 5/308 (1%)

Query: 3   PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62
           P IFIDG+ GTTGLQI  R+  RTD+ + ++  AER++A +R + +N+ DIAILCLPD A
Sbjct: 4   PVIFIDGDQGTTGLQIHERLRNRTDITVFTLAAAERKDARLRAEAINACDIAILCLPDAA 63

Query: 63  SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122
           +REAV  +  N  VR+ID S+AHR    W YGF EM   Q +RI  AR V NPGCYPTGA
Sbjct: 64  AREAVNAIV-NPAVRVIDASSAHRTQTGWTYGFPEMTSGQRERIASARRVTNPGCYPTGA 122

Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGLTLK 181
           I L+RPL QAG++PD YP++++AVSGY+G G+   A +E+ + PD I AP F +YGL L 
Sbjct: 123 IGLLRPLLQAGLIPDNYPISIHAVSGYSGRGR---AGVEEHEGPDAINAPSFQVYGLDLA 179

Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241
           HKH PE++ H LL + P+F P+ G F QG+++ VPL L  LA G    T+H  L  HYA 
Sbjct: 180 HKHTPEIQQHALLAQRPIFVPAYGAFRQGIVLTVPLQLRLLAPGVDGATLHTCLARHYAE 239

Query: 242 QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAV 301
            + V VVPL ES     +D   L G++ M+L VF      HV L A+ DNLGKGASGAAV
Sbjct: 240 AAHVRVVPLHESCAEKHLDPQVLNGTNDMRLSVFPAVDHGHVLLSAVFDNLGKGASGAAV 299

Query: 302 QNMDLMLS 309
           QN++LML+
Sbjct: 300 QNLNLMLT 307


Lambda     K      H
   0.319    0.136    0.395 

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: 327
Number of extensions: 18
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: 310
Length of database: 309
Length adjustment: 27
Effective length of query: 283
Effective length of database: 282
Effective search space:    79806
Effective search space used:    79806
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 H281DRAFT_02654 H281DRAFT_02654 (N-acetyl-gamma-glutamyl-phosphate reductase)
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.15799.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.8e-121  390.1   0.0   4.2e-121  390.0   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02654  H281DRAFT_02654 N-acetyl-gamma-g


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02654  H281DRAFT_02654 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.0   0.0  4.2e-121  4.2e-121       2     308 ..       4     306 ..       3     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 390.0 bits;  conditional E-value: 4.2e-121
                                    TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavs 67 
                                                  p +fidG++GttGlqi+erl +r+d+ + ++++  rkda  ra+ +na d+ailclpd aareav 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02654   4 PVIFIDGDQGTTGLQIHERLRNRTDITVFTLAAAERKDARLRAEAINACDIAILCLPDAAAREAVN 69 
                                                  78**************************************************************** PP

                                    TIGR01851  68 lvdnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGil 133
                                                   + np+++++das+a+rt+ +w+yGfpe++++qre+ia+a+rv+nPGcy+tgai llrPl++aG++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02654  70 AIVNPAVRVIDASSAHRTQTGWTYGFPEMTSGQRERIASARRVTNPGCYPTGAIGLLRPLLQAGLI 135
                                                  ****************************************************************** PP

                                    TIGR01851 134 PadfPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPift 199
                                                  P ++P++i+avsGysG G+a ++++e   a   +  +f++ygl l hkh pe+++h+ la++Pif+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02654 136 PDNYPISIHAVSGYSGRGRAGVEEHEGPDA--INAPSFQVYGLDLAHKHTPEIQQHALLAQRPIFV 199
                                                  **************************5544..44589***************************** PP

                                    TIGR01851 200 PavGdfaqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqgln 265
                                                  Pa G f qG+++++pl+l  l+  v ++ +h  la +y+  ++v+v++l+++    ++ ld+q ln
  lcl|FitnessBrowser__Burk376:H281DRAFT_02654 200 PAYGAFRQGIVLTVPLQLRLLAPGVDGATLHTCLARHYAEAAHVRVVPLHESC--AEKHLDPQVLN 263
                                                  **************************************************998..679******** PP

                                    TIGR01851 266 gtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnial 308
                                                  gtn + l vf++ d +++ll a +dnlGkGasGaavqnln++l
  lcl|FitnessBrowser__Burk376:H281DRAFT_02654 264 GTNDMRLSVFPAVDHGHVLLSAVFDNLGKGASGAAVQNLNLML 306
                                                  ******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (309 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.94
//
[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