Alignments for a candidate for argC in Thiothrix lacustris DSM 21227

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Thiothrix lacustris DSM 21227

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_028490259.1 Q394_RS0116805 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000621325.1:WP_028490259.1
          Length = 346

 Score =  431 bits (1109), Expect = e-125
 Identities = 212/343 (61%), Positives = 255/343 (74%)

Query: 46  KVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPDV 105
           K+GIVG TGYTGVELLR+L  HP+V ++C+TSR  AG  V  M+PNLRG+ DLAF+ P  
Sbjct: 4   KIGIVGATGYTGVELLRLLVSHPDVEITCVTSREHAGSRVDAMFPNLRGYLDLAFTAPSD 63

Query: 106 NVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPEW 165
             L ACDLVFFATP+GVAM+    L+ AG +V+DL+ADFR+KD+ +W  WYGM H SP  
Sbjct: 64  EALSACDLVFFATPNGVAMKSTQTLLDAGTKVIDLAADFRIKDIAIWEKWYGMQHASPNL 123

Query: 166 AEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGASG 225
            E+AVYGLPE+ R+ IR A+LVANPGCYPTAV LG LPL+E GL+D + +IAD KSG SG
Sbjct: 124 VEEAVYGLPELNREHIRQARLVANPGCYPTAVTLGLLPLVENGLIDLEGIIADTKSGVSG 183

Query: 226 AGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGIE 285
           AGR+ ++  L  E G++FKAY  +GHRH PEI Q L   A   +   FVPHL+PMIRGI 
Sbjct: 184 AGRKAEVHALLAEAGDNFKAYAVAGHRHQPEIAQTLSTVAQISIDPVFVPHLLPMIRGIH 243

Query: 286 ATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQEQS 345
           ATLYA L   A    LQ L+  R+ +EPFVDVMP GSHPETRSVRGAN CRMA+HR   +
Sbjct: 244 ATLYAMLSVEAAQADLQQLYTTRYANEPFVDVMPAGSHPETRSVRGANVCRMAIHRPGNA 303

Query: 346 NIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
             V+V SVIDNLVKGAAGQAVQNMN+M GL E + L+ P LLP
Sbjct: 304 RRVVVLSVIDNLVKGAAGQAVQNMNLMLGLSEHIALQQPGLLP 346


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: 384
Number of extensions: 9
Number of successful extensions: 1
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: 346
Length adjustment: 30
Effective length of query: 358
Effective length of database: 316
Effective search space:   113128
Effective search space used:   113128
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 WP_028490259.1 Q394_RS0116805 (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.27239.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-136  441.6   0.0   1.2e-136  441.4   0.0    1.0  1  lcl|NCBI__GCF_000621325.1:WP_028490259.1  Q394_RS0116805 N-acetyl-gamma-gl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000621325.1:WP_028490259.1  Q394_RS0116805 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.4   0.0  1.2e-136  1.2e-136       2     345 .]       4     346 .]       3     346 .] 0.98

  Alignments for each domain:
  == domain 1  score: 441.4 bits;  conditional E-value: 1.2e-136
                                 TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvdlkleeleeeeileead 69 
                                               k++ivGa+GYtG+eLlrll +Hp+ve+t +v+sre ag+++++++p+l+g +dl +++ ++e +l+++d
  lcl|NCBI__GCF_000621325.1:WP_028490259.1   4 KIGIVGATGYTGVELLRLLVSHPDVEIT-CVTSREhAGSRVDAMFPNLRGYLDLAFTAPSDE-ALSACD 70 
                                               79**************************.7777777*********************98887.567*** PP

                                 TIGR01850  70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138
                                               +vf+A+p+gv+++  ++ll++g+kvidl+adfR+kd +++ekwYg++h++++l+eeavYGlpElnre+i
  lcl|NCBI__GCF_000621325.1:WP_028490259.1  71 LVFFATPNGVAMKSTQTLLDAGTKVIDLAADFRIKDIAIWEKWYGMQHASPNLVEEAVYGLPELNREHI 139
                                               ********************************************************************* PP

                                 TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207
                                               ++a+l+anPGCy+Ta++L+l Pl++++li+ + ii d ksGvSgAGrka+ + l+ae+ +n+k+Y+v++
  lcl|NCBI__GCF_000621325.1:WP_028490259.1 140 RQARLVANPGCYPTAVTLGLLPLVENGLIDLEGIIADTKSGVSGAGRKAEVHALLAEAGDNFKAYAVAG 208
                                               ********************************************************************* PP

                                 TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276
                                               HrH+pEi+q+ls++a+ ++   f+phl+pm+rGi+at+ya l+ e  +++l++ly+++Y++epfv+v++
  lcl|NCBI__GCF_000621325.1:WP_028490259.1 209 HRHQPEIAQTLSTVAQISIDPVFVPHLLPMIRGIHATLYAMLSVEAAQADLQQLYTTRYANEPFVDVMP 277
                                               ************9998899999*********************************************** PP

                                 TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                               +g+ P+t++v+g n+++++++   +++rvvv+s+iDNLvKGaagqAvqn+Nlmlg++e+ +L++ +llp
  lcl|NCBI__GCF_000621325.1:WP_028490259.1 278 AGSHPETRSVRGANVCRMAIHRPGNARRVVVLSVIDNLVKGAAGQAVQNMNLMLGLSEHIALQQPGLLP 346
                                               ****************************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (346 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: 7.61
//
[ok]

This GapMind analysis is from Apr 10 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