Alignments for a candidate for argC in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Dinoroseobacter shibae DFL-12

Align Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplastic; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate 3608357 Dshi_1759 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= SwissProt::Q93Z70
         (401 letters)



>FitnessBrowser__Dino:3608357
          Length = 341

 Score =  367 bits (943), Expect = e-106
 Identities = 189/342 (55%), Positives = 242/342 (70%), Gaps = 5/342 (1%)

Query: 61  IGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVKDA 120
           I +LGASGYTGAE+VRL+A HP  ++T ++ADRKAGQ+M +VFPHLR   LP LV + D 
Sbjct: 4   IAILGASGYTGAELVRLIATHPRMRITALSADRKAGQTMGAVFPHLRHLDLPALVKIDDI 63

Query: 121 DFSTVDAVFCCLPHGTTQEIIKELPTALKIVDLSADFRLRNIAEYEEWYGQPHKAVELQK 180
           DF  VD VFC LPH T+Q +I  LP ++KIVDLSADFRLR+   Y +WYG PH A++LQ 
Sbjct: 64  DFGGVDLVFCALPHATSQSVIAALPKSVKIVDLSADFRLRDPEAYAKWYGGPHAALDLQA 123

Query: 181 EVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGVSGAG 240
           E VYGLTE  RE I+ ARLVA  GC   T Q  L PL+ A +I  + IIID K+GVSGAG
Sbjct: 124 EAVYGLTEFYREQIRDARLVAGTGCNAATGQYALRPLIAAGVIDLDEIIIDLKTGVSGAG 183

Query: 241 RGAKEANLYSEIAEGISSYGV-TRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGMQS 299
           R  KE  L++E++EG  +Y V   HRH+ E +Q  S +A  ++ V FTPHL+P  RG+ +
Sbjct: 184 RSLKENLLHAELSEGAHAYAVGGMHRHLGEFDQEFSALAGREIKVQFTPHLLPANRGILA 243

Query: 300 TIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPDRIPG 359
           T+YV+   G  TE ++  L  +YEDE FV +L EG  P T +VRGSN+ H+ V  DRIPG
Sbjct: 244 TVYVK---GEATE-IYDALADAYEDEPFVVMLPEGEHPSTRHVRGSNFVHIGVVRDRIPG 299

Query: 360 RAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401
           RA++I+ +DNL KG+SGQALQN N+ML   ETTGL+  P+FP
Sbjct: 300 RAVVIAALDNLTKGSSGQALQNANLMLDIEETTGLMMTPVFP 341


Lambda     K      H
   0.318    0.134    0.386 

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: 412
Number of extensions: 11
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: 401
Length of database: 341
Length adjustment: 30
Effective length of query: 371
Effective length of database: 311
Effective search space:   115381
Effective search space used:   115381
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 3608357 Dshi_1759 (N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq))
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.17208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.9e-118  379.4   0.0     1e-117  379.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608357  Dshi_1759 N-acetyl-gamma-glutamy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608357  Dshi_1759 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.2   0.0    1e-117    1e-117       2     345 .]       3     341 .]       2     341 .] 0.97

  Alignments for each domain:
  == domain 1  score: 379.2 bits;  conditional E-value: 1e-117
                         TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflAlphg 78 
                                       ++ai+GasGYtGaeL+rl+a+Hp++++t+l ++r+ag+++ +v+phl++l    l ++++ +    +d+vf+Alph 
  lcl|FitnessBrowser__Dino:3608357   3 NIAILGASGYTGAELVRLIATHPRMRITALSADRKAGQTMGAVFPHLRHLDLPALVKIDDID-FGGVDLVFCALPHA 78 
                                       79***********************************************9987777777754.569*********** PP

                         TIGR01850  79 vsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTaal 155
                                       +s++++ ++l k+vk++dlSadfRl+d+e+Y+kwYg +h++ +l++eavYGl+E++re+i++a+l+a  GC+a + +
  lcl|FitnessBrowser__Dino:3608357  79 TSQSVI-AALPKSVKIVDLSADFRLRDPEAYAKWYGGPHAALDLQAEAVYGLTEFYREQIRDARLVAGTGCNAATGQ 154
                                       ******.567888**************************************************************** PP

                         TIGR01850 156 LalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.kHrHtpEieqelsklaekkvkvsft 231
                                        al Pl+++++i+ ++ii+d k+GvSgAGr+ +e+ l+ae++e  ++Y+v   HrH  E  qe s+la++++kv+ft
  lcl|FitnessBrowser__Dino:3608357 155 YALRPLIAAGVIDLDEIIIDLKTGVSGAGRSLKENLLHAELSEGAHAYAVGgMHRHLGEFDQEFSALAGREIKVQFT 231
                                       **************************************************989************************ PP

                         TIGR01850 232 phlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvv 308
                                       phl+p  rGilat+y+k ++    +e++++++++Yedepfv +l+ege Pst++v+gsnfv+igv  d+  +r+vv+
  lcl|FitnessBrowser__Dino:3608357 232 PHLLPANRGILATVYVKGEA----TEIYDALADAYEDEPFVVMLPEGEHPSTRHVRGSNFVHIGVVRDRIPGRAVVI 304
                                       *****************998....89*************************************************** PP

                         TIGR01850 309 saiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                       +a+DNL+KG +gqA+qn Nlml+ +et+gL ++p++p
  lcl|FitnessBrowser__Dino:3608357 305 AALDNLTKGSSGQALQNANLMLDIEETTGLMMTPVFP 341
                                       **********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (341 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.41
//
[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