GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Synechococcus elongatus PCC 7942

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate Synpcc7942_1433 Synpcc7942_1433 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__SynE:Synpcc7942_1433
          Length = 352

 Score =  291 bits (744), Expect = 3e-83
 Identities = 148/350 (42%), Positives = 214/350 (61%), Gaps = 2/350 (0%)

Query: 41  EKMVIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAF 100
           E   + VGI+G +GY GV+L+R+L  HP++ V+ +     AG   AE+YP+L  H +L  
Sbjct: 3   ESSRLPVGIIGASGYGGVQLVRLLQDHPQLEVAYLGGDRSAGKEFAELYPHLGPHLNLTI 62

Query: 101 SEPDVN-VLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMA 159
              DV+ +   C  VF + P+G+A  + P L+  G +V+DLSAD+R  DL  +A WYG  
Sbjct: 63  EAIDVDRIAERCAAVFLSLPNGLAYDLAPALLERGCKVLDLSADYRFHDLKTYALWYGGD 122

Query: 160 HESPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADA 219
            +    A  A+YGLPE+ R+ I NAQL+  PGCYPTA  L   P L+QGL+DP  ++ DA
Sbjct: 123 RQDAAVAHTAIYGLPELYRNRIANAQLIGCPGCYPTASLLALAPALKQGLIDPDTIVIDA 182

Query: 220 KSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIP 279
           KSG SGAGRQ K   L  E G S  AYG + HRH PEI Q     +G +V + F PHL+P
Sbjct: 183 KSGTSGAGRQAKTNALLAEAGNSVGAYGVARHRHTPEIEQICSDLSGHEVLLQFTPHLMP 242

Query: 280 MIRGIEATLYAELKNP-ADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMA 338
           M+RGI AT+YA+L++P    +    +++  + + P V V+  G++P+T+   G N C + 
Sbjct: 243 MVRGIHATIYAKLRDPNLTTEDCLTVYQAFYRNAPMVKVLTHGTYPQTKWAAGTNLCYLG 302

Query: 339 LHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           L    ++  +++ S IDNL+KG AGQA+Q +N+M G +E +GL      P
Sbjct: 303 LEVDARTGRIVLLSAIDNLIKGQAGQAIQCLNLMQGWEEGLGLPTLCYYP 352


Lambda     K      H
   0.321    0.137    0.412 

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: 386
Number of extensions: 13
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: 388
Length of database: 352
Length adjustment: 30
Effective length of query: 358
Effective length of database: 322
Effective search space:   115276
Effective search space used:   115276
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 Synpcc7942_1433 Synpcc7942_1433 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01850 (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/TIGR01850.hmm
# target sequence database:        /tmp/gapView.9446.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01850  [M=345]
Accession:   TIGR01850
Description: argC: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-135  436.2   0.0   5.2e-135  436.0   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1433  Synpcc7942_1433 N-acetyl-gamma-g


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1433  Synpcc7942_1433 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.0   0.0  5.2e-135  5.2e-135       3     345 .]       9     352 .]       7     352 .] 0.99

  Alignments for each domain:
  == domain 1  score: 436.0 bits;  conditional E-value: 5.2e-135
                                 TIGR01850   3 vaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvv 71 
                                               v+i+GasGY+G++L+rll++Hp++ev++l ++r+agk+++e++phl  +++l++e++++++i+e++ +v
  lcl|FitnessBrowser__SynE:Synpcc7942_1433   9 VGIIGASGYGGVQLVRLLQDHPQLEVAYLGGDRSAGKEFAELYPHLGPHLNLTIEAIDVDRIAERCAAV 77 
                                               99******************************************************************* PP

                                 TIGR01850  72 flAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikk 140
                                               fl+lp+g +++l+p+lle+g+kv+dlSad+R++d ++Y+ wYg ++++ +++++a+YGlpEl+r++i++
  lcl|FitnessBrowser__SynE:Synpcc7942_1433  78 FLSLPNGLAYDLAPALLERGCKVLDLSADYRFHDLKTYALWYGGDRQDAAVAHTAIYGLPELYRNRIAN 146
                                               ********************************************************************* PP

                                 TIGR01850 141 aklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHr 209
                                               a+li++PGCy+Ta+lLalaP+lk++li+p++i++daksG+SgAGr+a+++ l+ae+ +++ +Y v++Hr
  lcl|FitnessBrowser__SynE:Synpcc7942_1433 147 AQLIGCPGCYPTASLLALAPALKQGLIDPDTIVIDAKSGTSGAGRQAKTNALLAEAGNSVGAYGVARHR 215
                                               ********************************************************************* PP

                                 TIGR01850 210 HtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkke.lteeelrklyeevYedepfvrvlke 277
                                               HtpEieq +s+l++++v ++ftphl+pm+rGi+atiyakl+++ lt+e+  ++y+++Y++ p+v+vl++
  lcl|FitnessBrowser__SynE:Synpcc7942_1433 216 HTPEIEQICSDLSGHEVLLQFTPHLMPMVRGIHATIYAKLRDPnLTTEDCLTVYQAFYRNAPMVKVLTH 284
                                               ****************************************9977************************* PP

                                 TIGR01850 278 gelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                               g++P+tk+ +g+n + +g++vd +t+r+v++saiDNL+KG+agqA+q+lNlm g++e  gL++l ++p
  lcl|FitnessBrowser__SynE:Synpcc7942_1433 285 GTYPQTKWAAGTNLCYLGLEVDARTGRIVLLSAIDNLIKGQAGQAIQCLNLMQGWEEGLGLPTLCYYP 352
                                               **************************************************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (352 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: 00:00:00.01
# Mc/sec: 9.67
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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