Alignments for a candidate for argC in Methanococcus aeolicus Nankai-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Methanococcus aeolicus Nankai-3

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate WP_011974022.1 MAEO_RS06695 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:Q58496
         (341 letters)



>NCBI__GCF_000017185.1:WP_011974022.1
          Length = 344

 Score =  452 bits (1162), Expect = e-132
 Identities = 228/346 (65%), Positives = 272/346 (78%), Gaps = 7/346 (2%)

Query: 1   MKEVAIIGATGYTGAELLRLLANHEKVNVTYITSRKEAGKHVFKVHPHLKGIEKYKNLCF 60
           M  ++IIG TGYTG+ELLR+L NH +V + +ITSRK  G ++ KVHP+LK I+   NL F
Sbjct: 1   MVTISIIGGTGYTGSELLRILLNHPQVEIKHITSRKMDGVNITKVHPNLKNIKNIDNLVF 60

Query: 61  TG-DIDKVDAYLVFTATPHGASMDIVPDFIERGMKVIDLSGDYRFEDLSLYEKYYKIKHK 119
                  +D+  VF ATPHGASM IVP+  E G K+IDLSGDYRFEDLSLYEK+Y + H 
Sbjct: 61  ENISPSNLDSDFVFCATPHGASMKIVPELYETGSKIIDLSGDYRFEDLSLYEKWYNLTHT 120

Query: 120 GLPDVKIAYGLPELHREEIKEAQLVANPGCFPTGAILAVAPLVKENIIEERIIFDSKTGV 179
           G  ++   YGLPELHR EIK+AQLVANPGCFPTG+ILA+APLVKE IIE RII DSKTGV
Sbjct: 121 G--ELPAVYGLPELHRNEIKKAQLVANPGCFPTGSILALAPLVKEGIIENRIIVDSKTGV 178

Query: 180 SGAGIKPTETTHFPNVNENINPYKITTHRHTPEIEKELKKL---GKAKVSFTPHLAPITR 236
           SGAG+ P+ETTH+P+VNENI PYK+TTHRH+PEIEKEL+KL      K+SFTPHLAP+TR
Sbjct: 179 SGAGVNPSETTHYPSVNENILPYKMTTHRHSPEIEKELEKLNISNNIKLSFTPHLAPLTR 238

Query: 237 GILTTAHTFLAK-DVDREEIIKIYEKFYGSEVFVRIFSEEIPKLTWVRGTNFCDIGGFEI 295
           GIL+T H++L   D+DR+ II IY +FY +E FVRIF E  P LT VRG+NFCDIGGFEI
Sbjct: 239 GILSTTHSYLKNTDIDRDIIIDIYNEFYKNEPFVRIFEEGAPTLTGVRGSNFCDIGGFEI 298

Query: 296 DEHGRLVVISAIDNLVKGASGQAIQNMNIMFGFDEKEGLFDVGLNP 341
           D HGR+VV+SAIDNLVKGASGQAI N+N+M GF+E E L   GL P
Sbjct: 299 DRHGRIVVVSAIDNLVKGASGQAIHNLNLMAGFNETESLLYGGLKP 344


Lambda     K      H
   0.319    0.140    0.409 

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: 499
Number of extensions: 22
Number of successful extensions: 5
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: 341
Length of database: 344
Length adjustment: 29
Effective length of query: 312
Effective length of database: 315
Effective search space:    98280
Effective search space used:    98280
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_011974022.1 MAEO_RS06695 (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.384.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-132  427.7   0.0     2e-132  427.6   0.0    1.0  1  lcl|NCBI__GCF_000017185.1:WP_011974022.1  MAEO_RS06695 N-acetyl-gamma-glut


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017185.1:WP_011974022.1  MAEO_RS06695 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.6   0.0    2e-132    2e-132       2     345 .]       3     344 .]       2     344 .] 0.94

  Alignments for each domain:
  == domain 1  score: 427.6 bits;  conditional E-value: 2e-132
                                 TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeileead 69 
                                               +++i+G++GYtG eLlr+l +Hp+ve+++++s++  g ++++vhp+lk++ +  +l  ++++  + + d
  lcl|NCBI__GCF_000017185.1:WP_011974022.1   3 TISIIGGTGYTGSELLRILLNHPQVEIKHITSRKMDGVNITKVHPNLKNIKNiDNLVFENISPSNLDSD 71 
                                               789*************************6655555*************9988777777777666789** PP

                                 TIGR01850  70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138
                                               +vf+A+phg+s+++vpel+e+g k+idlS+d+R++d ++YekwY+ +h+ e     avYGlpEl+r+ei
  lcl|NCBI__GCF_000017185.1:WP_011974022.1  72 FVFCATPHGASMKIVPELYETGSKIIDLSGDYRFEDLSLYEKWYNLTHTGE---LPAVYGLPELHRNEI 137
                                               *************************************************95...68************* PP

                                 TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207
                                               kka+l+anPGC++T+++LalaPl+ke++ie+ +iivd+k+GvSgAG ++se+++++ vnen+ pYk+t+
  lcl|NCBI__GCF_000017185.1:WP_011974022.1 138 KKAQLVANPGCFPTGSILALAPLVKEGIIEN-RIIVDSKTGVSGAGVNPSETTHYPSVNENILPYKMTT 205
                                               ***************************9998.5************************************ PP

                                 TIGR01850 208 HrHtpEieqelsklaek.kvkvsftphlvpmtrGilatiyaklkke.lteeelrklyeevYedepfvrv 274
                                               HrH pEie+el+kl+ + ++k+sftphl+p+trGil+t++  lk+  ++++ + ++y+e+Y++epfvr+
  lcl|NCBI__GCF_000017185.1:WP_011974022.1 206 HRHSPEIEKELEKLNISnNIKLSFTPHLAPLTRGILSTTHSYLKNTdIDRDIIIDIYNEFYKNEPFVRI 274
                                               *************99776899********************99987699999***************** PP

                                 TIGR01850 275 lkegelPstkavlgsnfvdig.vavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342
                                               ++ + +P+++ v+gsnf+dig +++d +++r+vvvsaiDNLvKGa+gqA+ nlNlm gf+ete+L + +
  lcl|NCBI__GCF_000017185.1:WP_011974022.1 275 FE-EGAPTLTGVRGSNFCDIGgFEID-RHGRIVVVSAIDNLVKGASGQAIHNLNLMAGFNETESLLYGG 341
                                               *8.899***************55555.59************************************9877 PP

                                 TIGR01850 343 llp 345
                                               l p
  lcl|NCBI__GCF_000017185.1:WP_011974022.1 342 LKP 344
                                               765 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: 10.89
//
[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