Alignments for a candidate for argC in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Pseudomonas fluorescens FW300-N2C3

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 AO356_14490 AO356_14490 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q93Z70
         (401 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14490
          Length = 344

 Score =  313 bits (801), Expect = 6e-90
 Identities = 163/345 (47%), Positives = 220/345 (63%), Gaps = 4/345 (1%)

Query: 59  IRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVK 118
           +++G++G +GYTG E++RLLA HP  +V ++T+  +AG ++  ++P+LR        SV 
Sbjct: 2   VKVGIVGGTGYTGVELLRLLAQHPQAEVVVITSRSEAGLAVADMYPNLRGHYDGLAFSVP 61

Query: 119 DAD-FSTVDAVFCCLPHGTTQEIIKELPTA-LKIVDLSADFRLRNIAEYEEWYGQPHKAV 176
           D       D VF   PHG    +  EL  A  K++DLSADFRL++  E+ +WYGQPH A 
Sbjct: 62  DVKTLGACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGAP 121

Query: 177 ELQKEVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGV 236
           EL +E VYGL E+ RE IK+ARL+A PGCYPT  QL  +PLL+A L     +I D KSGV
Sbjct: 122 ELLEEAVYGLPEVNREKIKQARLIAVPGCYPTATQLGFLPLLEAGLADTSRLIADCKSGV 181

Query: 237 SGAGRGAKEANLYSEIAEGISSYGVTRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRG 296
           SGAGRGA   +LYSE +E + +Y V  HRH+PEI QGL   A   V ++F PHL PMIRG
Sbjct: 182 SGAGRGASVGSLYSETSESMKAYAVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTPMIRG 241

Query: 297 MQSTIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPDR 356
           + ST+Y  +    R+ DL    +  Y +E FV V+  G  P T +VRG+N C ++V   +
Sbjct: 242 IHSTLYATVVD--RSVDLQALFEKRYANEPFVDVMPAGSHPETRSVRGANVCRIAVHRPQ 299

Query: 357 IPGRAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401
                +++SVIDNLVKGASGQA+QNLNI+ G  E  GL H  + P
Sbjct: 300 DGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERLGLSHAGMLP 344


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: 408
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: 401
Length of database: 344
Length adjustment: 30
Effective length of query: 371
Effective length of database: 314
Effective search space:   116494
Effective search space used:   116494
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 AO356_14490 AO356_14490 (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.12690.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.5e-136  441.1   0.0   1.7e-136  440.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490  AO356_14490 N-acetyl-gamma-gluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490  AO356_14490 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.9   0.0  1.7e-136  1.7e-136       1     345 []       2     344 .]       2     344 .] 0.98

  Alignments for each domain:
  == domain 1  score: 440.9 bits;  conditional E-value: 1.7e-136
                                       TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleee 62 
                                                     +kv+ivG++GYtG+eLlrlla+Hp++ev+ ++s++eag  +++++p+l+g++d l ++  +++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490   2 VKVGIVGGTGYTGVELLRLLAQHPQAEVVVITSRSEAGLAVADMYPNLRGHYDgLAFSVPDVK 64 
                                                     69***************************8888888*****************8888877666 PP

                                       TIGR01850  63 eileeadvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeellee 125
                                                      +l ++dvvf+A+phgv+++l+ ell++g+kvidlSadfRl+da++++kwYg++h ++ellee
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490  65 -TLGACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGAPELLEE 126
                                                     .677*********************************************************** PP

                                       TIGR01850 126 avYGlpElnreeikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkas 188
                                                     avYGlpE+nre+ik+a+lia+PGCy+Ta++L+  Pll+++l +++++i d+ksGvSgAGr as
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490 127 AVYGLPEVNREKIKQARLIAVPGCYPTATQLGFLPLLEAGLADTSRLIADCKSGVSGAGRGAS 189
                                                     *************************************************************** PP

                                       TIGR01850 189 ekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkk 251
                                                       sl++e++e++k+Y+v++HrH pEi+q l+++a+k+v ++f+phl+pm+rGi++t+ya++ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490 190 VGSLYSETSESMKAYAVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTPMIRGIHSTLYATVVD 252
                                                     **************************************************************9 PP

                                       TIGR01850 252 elteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNL 314
                                                       ++ +l++l+e++Y++epfv+v+++g+ P+t++v+g n+++i+v+  ++ + vvv+s+iDNL
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490 253 --RSVDLQALFEKRYANEPFVDVMPAGSHPETRSVRGANVCRIAVHRPQDGDLVVVLSVIDNL 313
                                                     ..789********************************************************** PP

                                       TIGR01850 315 vKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                                     vKGa+gqAvqnlN+ +g+de+ gL++ ++lp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14490 314 VKGASGQAVQNLNILFGLDERLGLSHAGMLP 344
                                                     **************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (344 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: 9.80
//
[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:

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, 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

GapMind for Amino acid biosynthesis