GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Trichormus variabilis ATCC 29413

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_011317428.1 AVA_RS02805 acetylglutamate kinase

Query= BRENDA::Q6V1L5
         (301 letters)



>NCBI__GCF_000204075.1:WP_011317428.1
          Length = 297

 Score =  435 bits (1118), Expect = e-127
 Identities = 215/290 (74%), Positives = 251/290 (86%)

Query: 4   EFIEAGAADRVRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMR 63
           E+I    A RV++LSEALPY+QQFAGRTVVVKYGGAAMK   LK+ V+RDIVFL+CVG+R
Sbjct: 7   EYIRQAEATRVQVLSEALPYIQQFAGRTVVVKYGGAAMKDSHLKDQVIRDIVFLSCVGLR 66

Query: 64  PVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGG 123
           P++VHGGGPEIN+WL ++GIE QF NGLRVTDA TM+VVEMVLVGRVNK+IVS IN  GG
Sbjct: 67  PILVHGGGPEINSWLDKLGIEAQFKNGLRVTDAPTMDVVEMVLVGRVNKEIVSLINQAGG 126

Query: 124 RAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQS 183
            AVG CG DG L+ ARP  QEGIGFVGEV++VN +++E L   GYIPV+SSVAAD++GQ+
Sbjct: 127 LAVGLCGKDGNLITARPQGQEGIGFVGEVSNVNIKILETLASNGYIPVVSSVAADDSGQA 186

Query: 184 FNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGG 243
           +NINADTVAGEIAAAL AEKLILLTDTRGIL+D K P +LIP+++I ++RELI  G+V G
Sbjct: 187 YNINADTVAGEIAAALGAEKLILLTDTRGILKDYKDPGTLIPKVDIREARELINGGVVSG 246

Query: 244 GMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMIVGSGY 293
           GMIPKV CC+RSLAQGVRAAHIIDGRIPHALLLEIFTD GIGTMI+GS Y
Sbjct: 247 GMIPKVTCCVRSLAQGVRAAHIIDGRIPHALLLEIFTDVGIGTMILGSQY 296


Lambda     K      H
   0.320    0.139    0.406 

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: 391
Number of extensions: 14
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: 301
Length of database: 297
Length adjustment: 27
Effective length of query: 274
Effective length of database: 270
Effective search space:    73980
Effective search space used:    73980
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: 48 (23.1 bits)

Align candidate WP_011317428.1 AVA_RS02805 (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.3443503.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-90  289.0   1.4    1.6e-90  288.7   1.4    1.1  1  NCBI__GCF_000204075.1:WP_011317428.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011317428.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.7   1.4   1.6e-90   1.6e-90       1     231 []      34     268 ..      34     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 288.7 bits;  conditional E-value: 1.6e-90
                             TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 
                                           t+V+K+GGaa++  +l++++++di++l  +g+++++vHGGgpein +l+klgie +f+nglRvTd+ t++vve
  NCBI__GCF_000204075.1:WP_011317428.1  34 TVVVKYGGAAMKdsHLKDQVIRDIVFLSCVGLRPILVHGGGPEINSWLDKLGIEAQFKNGLRVTDAPTMDVVE 106
                                           69*********98899********************************************************* PP

                             TIGR00761  72 mvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviasla 144
                                           mvl+g+vnke+v l++++g  avGl+gkDg+l+ta+   +e +g+vGe+++vn ++le+l  +g+ipv++s+a
  NCBI__GCF_000204075.1:WP_011317428.1 107 MVLVGRVNKEIVSLINQAGGLAVGLCGKDGNLITARPQGQEGIGFVGEVSNVNIKILETLASNGYIPVVSSVA 179
                                           ************************************999999******************************* PP

                             TIGR00761 145 ldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkksliseleleeieqlikqavikgGmipKv 215
                                           +d++gq++N+naDt+A+e+Aaal+AekL+lLtd++Gil++  d  +li +++++e+++li+ +v+ gGmipKv
  NCBI__GCF_000204075.1:WP_011317428.1 180 ADDSGQAYNINADTVAGEIAAALGAEKLILLTDTRGILKDykDPGTLIPKVDIREARELINGGVVSGGMIPKV 252
                                           ****************************************99999**************************** PP

                             TIGR00761 216 eaalealesgvkkvvi 231
                                           ++++++l++gv++++i
  NCBI__GCF_000204075.1:WP_011317428.1 253 TCCVRSLAQGVRAAHI 268
                                           **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (297 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: 13.05
//
[ok]

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

Links

Downloads

Related tools

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