GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Lacinutrix algicola AKS293

Align N-succinylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_055434902.1 ASC41_RS01635 N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Pedo557:CA265_RS18540
         (326 letters)



>NCBI__GCF_001418085.1:WP_055434902.1
          Length = 327

 Score =  406 bits (1043), Expect = e-118
 Identities = 202/325 (62%), Positives = 243/325 (74%)

Query: 2   KIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVSD 61
           K++ GIIGGAGYT GE++R+L+NHP   I F+ STSNAGN IS VH DLIG TDL+F S 
Sbjct: 3   KLEIGIIGGAGYTAGELIRLLLNHPKTNINFIYSTSNAGNKISKVHQDLIGSTDLEFSSQ 62

Query: 62  IPQDIDVLFLCVGHGDAKKFLTANPIKDNIKIIDLSQDFRLHANASFSTKDFVYGLPELN 121
           I  +++VLFLC+GHG++K FL  N      KIIDLS DFRL  +  F +K FVYGLPELN
Sbjct: 63  INSEVEVLFLCLGHGNSKAFLVKNSFSAETKIIDLSNDFRLTKDTIFDSKTFVYGLPELN 122

Query: 122 RDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNEVHINATTGSTGAGQSLSTTSHFSW 181
           ++ IK A  IANPGCFA+ IQL LLPLA   ++QN+VHINA TG+TGAG SLS T+HF+W
Sbjct: 123 KEAIKKANYIANPGCFASAIQLALLPLAEAEVLQNDVHINAVTGATGAGTSLSATTHFTW 182

Query: 182 RNNNLSIYKAFEHQHLNEISESLLQLQPSISEALNFIPQRGAFTRGILAAMYLESDLSLE 241
           R+NN S YKAF HQHL EI++S+  LQ   +  +NF+P RG F+RGI A MY +   SLE
Sbjct: 183 RDNNFSHYKAFTHQHLGEINQSVKLLQSDFNSDINFMPNRGDFSRGIFATMYTKFKGSLE 242

Query: 242 EAQNIYEAYYSAHPFTHVSRKNIDLKQVVNTNKALVHLEKHGGKLFIISIIDNLLKGASG 301
           +A+ +Y A+Y    FT VS   I LKQVVNTNK ++HL KH  KL + SIIDNLLKGASG
Sbjct: 243 DAKALYNAFYKDAAFTVVSDDEIHLKQVVNTNKCILHLHKHEDKLLVTSIIDNLLKGASG 302

Query: 302 QAVQNMNLMFGLDETAGLKLKAAYF 326
           QAVQNMNLMFG DET GLKLKA YF
Sbjct: 303 QAVQNMNLMFGFDETEGLKLKATYF 327


Lambda     K      H
   0.319    0.135    0.387 

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: 338
Number of extensions: 6
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: 326
Length of database: 327
Length adjustment: 28
Effective length of query: 298
Effective length of database: 299
Effective search space:    89102
Effective search space used:    89102
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: 48 (23.1 bits)

Align candidate WP_055434902.1 ASC41_RS01635 (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.1906557.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.7e-97  312.0   0.1    3.7e-97  311.5   0.1    1.1  1  NCBI__GCF_001418085.1:WP_055434902.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055434902.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.5   0.1   3.7e-97   3.7e-97       2     342 ..       5     324 ..       4     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 311.5 bits;  conditional E-value: 3.7e-97
                             TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflA 74 
                                           +++i+G+ GYt++eL+rll +Hp+++++ ++s+++ag+k+s+vh+ l g +dl++++    +i++e++v+fl+
  NCBI__GCF_001418085.1:WP_055434902.1   5 EIGIIGGAGYTAGELIRLLLNHPKTNINFIYSTSNAGNKISKVHQDLIGSTDLEFSS----QINSEVEVLFLC 73 
                                           699************************************************999995....57789******* PP

                             TIGR01850  75 lphgvsael.vpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146
                                           l hg s+++ v++  ++++k+idlS dfRl++ +++              +++vYGlpEln+e+ikka++ian
  NCBI__GCF_001418085.1:WP_055434902.1  74 LGHGNSKAFlVKNSFSAETKIIDLSNDFRLTKDTIFD------------SKTFVYGLPELNKEAIKKANYIAN 134
                                           ******986277888999*************886553............3689******************** PP

                             TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219
                                           PGC+a a++Lal Pl+++++++++ + ++a++G +gAG++ s++++f+ +++n++ Yk+++H+H  Ei+q+++
  NCBI__GCF_001418085.1:WP_055434902.1 135 PGCFASAIQLALLPLAEAEVLQND-VHINAVTGATGAGTSLSATTHFTWRDNNFSHYKAFTHQHLGEINQSVK 206
                                           *********************985.************************************************ PP

                             TIGR01850 220 klaek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnf 291
                                            l+++ +  ++f+p+  +++rGi+at+y+k+k +l  e+ ++ly+++Y+d  f  v + +e+ ++k+v+ +n 
  NCBI__GCF_001418085.1:WP_055434902.1 207 LLQSDfNSDINFMPNRGDFSRGIFATMYTKFKGSL--EDAKALYNAFYKDAAFTVVSD-DEI-HLKQVVNTNK 275
                                           999887777************************66..9999************99998.555.9********* PP

                             TIGR01850 292 vdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342
                                           + + ++ +e  ++++v+s iDNL+KGa+gqAvqn+Nlm+gfdetegL+ ++
  NCBI__GCF_001418085.1:WP_055434902.1 276 CILHLHKHE--DKLLVTSIIDNLLKGASGQAVQNMNLMFGFDETEGLKLKA 324
                                           *99888777..89**********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (327 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.26
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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:

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:

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:

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:

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