Alignments for a candidate for argC in Synechococcus elongatus PCC 7942

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.28111.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.45
//
[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