Alignments for a candidate for argC in Desulfurobacterium atlanticum DSM 15668

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Desulfurobacterium atlanticum DSM 15668

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 WP_089322546.1 CHB58_RS02605 N-acetyl-gamma-glutamyl-phosphate reductase

Query= SwissProt::Q6AV34
         (415 letters)



>NCBI__GCF_900188395.1:WP_089322546.1
          Length = 349

 Score =  264 bits (674), Expect = 4e-75
 Identities = 151/353 (42%), Positives = 211/353 (59%), Gaps = 16/353 (4%)

Query: 69  SGEEVRIAVLGASGYTGAEIVRLLANHPQFRIKVMTADRKAGEQFGSVFPHLITQDLPNL 128
           SG+ V I+++GASGYTGAE++RLL  HP   I  +T+ + AG++   VFPHL    +  L
Sbjct: 5   SGQNVNISIIGASGYTGAELLRLLLFHPFVNILSLTSRQYAGQKVSDVFPHLYGSKVSKL 64

Query: 129 VAVK---DADFSNVDAVFCCLPHGTTQEIIKGLPQ---ELKIVDLSADFRLRDINEYAEW 182
           V  +   D   S  D VF CLPH     +++GL +   ELKI+D SADFR      Y + 
Sbjct: 65  VFTEFNVDTVASMSDVVFVCLPHRAAFPVVRGLYEKKPELKIIDFSADFRFDSPEIYEKV 124

Query: 183 YGHSHRAPELQQEAVYGLTEVLRNEIRNARLVANPGCYPTSIQLPLVPLIKAKLIKVS-N 241
           YG  H A EL  +  YGL E+ R+EI+N  +VANPGCYPTS+ L L P   + LI  +  
Sbjct: 125 YGVKHHAKELFAKVAYGLPEIFRDEIKNKTIVANPGCYPTSVILGLYPAKISGLIDENYP 184

Query: 242 IIIDAKSGVSGAGRGAKEANLYTEIAEGIHAYGIKGHRHVPEIEQGLSEAAESKVTISFT 301
           +I D+KSGV+GAGR +  +  + E+ E   AY ++GHRH PEI + L     S   + FT
Sbjct: 185 VIADSKSGVTGAGRKSSVSFTFCEVNETFKAYAVEGHRHAPEIAEKL-----SLKKVRFT 239

Query: 302 PNLICMKRGMQSTMFVEMAPGVTANDLYQHLKSTYEGEEFVKLLNGSSVPHTRHVVGSNY 361
           P+L+ M RG+ ST++ +        +L       Y+ E+FV+L   S  P T HV G+N+
Sbjct: 240 PHLVPMNRGILSTIYFK--TDAAKEELQAVYNQFYKNEKFVRL--KSFPPETSHVAGTNF 295

Query: 362 CFMNVFEDRIPGRAIIISVIDNLVKGASGQAVQNLNLMMGLPENTGLQYQPLF 414
           C + V +D   G  + IS IDN+ KGASGQA+QN+N++ G PE+TGL    L+
Sbjct: 296 CDIYVTKDEETGLGVAISAIDNIGKGASGQAIQNMNILCGFPEDTGLNQYSLW 348


Lambda     K      H
   0.317    0.135    0.391 

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: 395
Number of extensions: 19
Number of successful extensions: 6
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: 415
Length of database: 349
Length adjustment: 30
Effective length of query: 385
Effective length of database: 319
Effective search space:   122815
Effective search space used:   122815
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: 50 (23.9 bits)

Align candidate WP_089322546.1 CHB58_RS02605 (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.874364.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.3e-122  393.0   0.0   7.8e-122  392.7   0.0    1.0  1  NCBI__GCF_900188395.1:WP_089322546.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188395.1:WP_089322546.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.7   0.0  7.8e-122  7.8e-122       2     343 ..      10     347 ..       9     348 .. 0.96

  Alignments for each domain:
  == domain 1  score: 392.7 bits;  conditional E-value: 7.8e-122
                             TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd..lkleeleeeeileeadvvf 72 
                                           +++i+GasGYtGaeLlrll  Hp v++ +l+s++ ag+k+s+v+phl g     l ++e++++++++  dvvf
  NCBI__GCF_900188395.1:WP_089322546.1  10 NISIIGASGYTGAELLRLLLFHPFVNILSLTSRQYAGQKVSDVFPHLYGSKVskLVFTEFNVDTVASMSDVVF 82 
                                           799*************************8877777************87654358899999999********* PP

                             TIGR01850  73 lAlphgvsaelvpellekg..vkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkakl 143
                                           ++lph+++ ++v+ l+ek+  +k+id SadfR++++e+Yek Yg kh+++el ++++YGlpE+ r+eik+ ++
  NCBI__GCF_900188395.1:WP_089322546.1  83 VCLPHRAAFPVVRGLYEKKpeLKIIDFSADFRFDSPEIYEKVYGVKHHAKELFAKVAYGLPEIFRDEIKNKTI 155
                                           ****************96666**************************************************** PP

                             TIGR01850 144 ianPGCyaTaalLalaPllkekliepks.iivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEie 215
                                           +anPGCy+T+++L+l+P+  ++li+++  +i d+ksGv+gAGrk s + +f+evne +k+Y+v++HrH+pEi+
  NCBI__GCF_900188395.1:WP_089322546.1 156 VANPGCYPTSVILGLYPAKISGLIDENYpVIADSKSGVTGAGRKSSVSFTFCEVNETFKAYAVEGHRHAPEIA 228
                                           **************************9999******************************************* PP

                             TIGR01850 216 qelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlg 288
                                           ++ls l     kv+ftphlvpm rGil+tiy+k+++   +eel+++y+++Y++e+fvr+ +    P+t++v+g
  NCBI__GCF_900188395.1:WP_089322546.1 229 EKLS-L----KKVRFTPHLVPMNRGILSTIYFKTDA--AKEELQAVYNQFYKNEKFVRLKS--FPPETSHVAG 292
                                           ****.3....369*******************9998..89******************997..89******** PP

                             TIGR01850 289 snfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpl 343
                                           +nf+di v+ deet+  v +saiDN+ KGa+gqA+qn+N+ +gf+e++gL++++l
  NCBI__GCF_900188395.1:WP_089322546.1 293 TNFCDIYVTKDEETGLGVAISAIDNIGKGASGQAIQNMNILCGFPEDTGLNQYSL 347
                                           **************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (349 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: 00:00:00.00
# Mc/sec: 13.96
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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