GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Pontibacter ramchanderi LP43

Align N-succinylglutamate kinase (EC 2.7.2.-) (characterized)
to candidate WP_101442813.1 BD749_RS02620 acetylglutamate kinase

Query= reanno::Btheta:352922
         (257 letters)



>NCBI__GCF_002846395.1:WP_101442813.1
          Length = 265

 Score =  265 bits (676), Expect = 9e-76
 Identities = 134/250 (53%), Positives = 177/250 (70%), Gaps = 3/250 (1%)

Query: 7   VIKVGGKIVEEEATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVNGRRITD 66
           +IK+GG ++++   L + L DFA +SG K+LVHGGG+ A+ I  +LGI    V GRR+TD
Sbjct: 3   IIKIGGNVLDKPERLQRFLIDFAQLSGLKLLVHGGGKIASTIGLRLGIAPAYVEGRRLTD 62

Query: 67  AETLKVVTMVYGGLVNKNIVAGLQARGVNALGLTGADMNVIRSVKRPVKEVDYGFVGDV- 125
           AETL+VVTMVYGGL+NKN+VA LQA G NA+G+TGAD N I + KRPVK VDYG+ GD+ 
Sbjct: 63  AETLQVVTMVYGGLINKNVVAQLQALGCNAIGMTGADANAIPATKRPVKTVDYGYAGDIA 122

Query: 126 --EKVDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTIAGETAKALSALFDVTLVYC 183
             E ++A+ +  L+  G+ PV APLTHDG GNMLNTNADTIA   A AL+  ++V LVYC
Sbjct: 123 GPETINATAIRALLSAGLTPVFAPLTHDGHGNMLNTNADTIASVLATALAPHYNVQLVYC 182

Query: 184 FEKKGVLRDENDDDSVIPEITRAEFEQYVADGVIQGGMIPKLENSFEAINAGVTEVVITL 243
           FEKKGVL D +DD+SVI  I    +++    G++  GMIPKL+N+F A+  GV  V+I  
Sbjct: 183 FEKKGVLADASDDNSVISHIDENRYKELKEKGIVTDGMIPKLDNAFAALRQGVKAVLIGE 242

Query: 244 ASAIKDNEGT 253
           A  +    G+
Sbjct: 243 AEGLASLAGS 252


Lambda     K      H
   0.316    0.135    0.366 

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: 247
Number of extensions: 9
Number of successful extensions: 2
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: 257
Length of database: 265
Length adjustment: 25
Effective length of query: 232
Effective length of database: 240
Effective search space:    55680
Effective search space used:    55680
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 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate WP_101442813.1 BD749_RS02620 (acetylglutamate kinase)
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))

# 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/TIGR00761.hmm
# target sequence database:        /tmp/gapView.3185176.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00761  [M=231]
Accession:   TIGR00761
Description: argB: acetylglutamate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.6e-59  186.1   0.6    4.1e-59  185.9   0.6    1.0  1  NCBI__GCF_002846395.1:WP_101442813.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101442813.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.9   0.6   4.1e-59   4.1e-59       1     231 []       1     240 [.       1     240 [. 0.91

  Alignments for each domain:
  == domain 1  score: 185.9 bits;  conditional E-value: 4.1e-59
                             TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 
                                           + +iKiGG++++  e l++++ d a+   +g+k ++vHGGg+  +++  +lgi + +v+g R+Td+etl+vv+
  NCBI__GCF_002846395.1:WP_101442813.1   1 MYIIKIGGNVLDkpERLQRFLIDFAQ--LSGLK-LLVHGGGKIASTIGLRLGIAPAYVEGRRLTDAETLQVVT 70 
                                           679*********44444555444444..45677.89************************************* PP

                             TIGR00761  72 mvligkvnkelvallekhgikavGltgkDgqlltae..kldkedlgyvGei...kkvnkelleallkagiipv 139
                                           mv+ g +nk++va+l+  g++a+G+tg+D++ + a+   ++  d+gy G+i   + +n+ +++all ag +pv
  NCBI__GCF_002846395.1:WP_101442813.1  71 MVYGGLINKNVVAQLQALGCNAIGMTGADANAIPATkrPVKTVDYGYAGDIagpETINATAIRALLSAGLTPV 143
                                           ***********************************955455559*****9855579***************** PP

                             TIGR00761 140 iaslaldeegqllNvnaDtaAaelAaaleAe...kLvlLtdvaGileg..dkksliseleleeieqlikqavi 207
                                            a+l  d +g++lN+naDt+A+ lA+al ++   +Lv+  +++G+l++  d +s+is+++ +++++l +++++
  NCBI__GCF_002846395.1:WP_101442813.1 144 FAPLTHDGHGNMLNTNADTIASVLATALAPHynvQLVYCFEKKGVLADasDDNSVISHIDENRYKELKEKGIV 216
                                           ****************************9875557************9999999******************* PP

                             TIGR00761 208 kgGmipKveaalealesgvkkvvi 231
                                           ++GmipK+++a +al++gvk+v i
  NCBI__GCF_002846395.1:WP_101442813.1 217 TDGMIPKLDNAFAALRQGVKAVLI 240
                                           ********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (265 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.09
//
[ok]

This GapMind analysis is from Jul 26 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:

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