Aligments for a candidate for argB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for argB in Caulobacter crescentus NA1000

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate CCNA_00285 CCNA_00285 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__Caulo:CCNA_00285
          Length = 304

 Score =  280 bits (715), Expect = 4e-80
 Identities = 141/290 (48%), Positives = 209/290 (72%), Gaps = 6/290 (2%)

Query: 12  AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71
           AK L+EALPYI+ +  +T+VIKYGG+AM  E++   FA D VL+K +G++PVVVHGGGPQ
Sbjct: 13  AKTLAEALPYIQIYDRETVVIKYGGHAMGQEDVAKVFAADAVLLKLLGVHPVVVHGGGPQ 72

Query: 72  IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSA----IGLT 127
           I  +L +  ++S F+DG+RVTD ATM+V EMVL G +NK+I N I   G  A    +GL+
Sbjct: 73  ISRMLDKAGVKSTFVDGLRVTDEATMEVAEMVLSGAINKEIANWITLAGAEADVRGVGLS 132

Query: 128 GKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLV--KGDFIPVIAPI 185
           GKDA LI A+K+T T++ P+    + +D+G VGE T V+  L+  L+  + D+IPV+API
Sbjct: 133 GKDARLITAEKVTRTKKDPDSNIEQAVDLGFVGEPTKVDPQLIEALLTSEHDYIPVVAPI 192

Query: 186 GVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIAD 245
           GV  +G+++NINAD VAG +A ALKA+++++LT+I G++D  G+++  ++ EQ   LI  
Sbjct: 193 GVSPDGDTFNINADTVAGALAGALKAKRMLMLTDIKGVLDGNGELIREMTIEQARALIDT 252

Query: 246 GTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295
           G   GGM+PK+  A+ A++ GV +  I+DGR P+A+L+E+F++ G GTLI
Sbjct: 253 GVATGGMIPKLENAIHAIESGVEAVVILDGRRPHAMLVELFSEYGAGTLI 302


Lambda     K      H
   0.318    0.138    0.381 

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: 257
Number of extensions: 8
Number of successful extensions: 3
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: 304
Length adjustment: 27
Effective length of query: 274
Effective length of database: 277
Effective search space:    75898
Effective search space used:    75898
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: 48 (23.1 bits)

Align candidate CCNA_00285 CCNA_00285 (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.25229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.9e-77  245.3   5.2    3.4e-77  245.1   5.2    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00285  CCNA_00285 acetylglutamate kinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00285  CCNA_00285 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   5.2   3.4e-77   3.4e-77       1     231 []      30     279 ..      30     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 3.4e-77
                             TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 
                                           t+ViK+GG+a+   ++ + +a+d++ l+  g+++v+vHGGgp+i+++l+k g++  fv+glRvTd++t+ev+e
  lcl|FitnessBrowser__Caulo:CCNA_00285  30 TVVIKYGGHAMGqeDVAKVFAADAVLLKLLGVHPVVVHGGGPQISRMLDKAGVKSTFVDGLRVTDEATMEVAE 102
                                           69*********98899999****************************************************** PP

                             TIGR00761  72 mvligkvnkelvallekhgika....vGltgkDgqlltaekldke............dlgyvGeikkvnkell 128
                                           mvl g +nke+ ++++ +g++a    vGl+gkD++l+taek+++             dlg+vGe +kv+++l+
  lcl|FitnessBrowser__Caulo:CCNA_00285 103 MVLSGAINKEIANWITLAGAEAdvrgVGLSGKDARLITAEKVTRTkkdpdsnieqavDLGFVGEPTKVDPQLI 175
                                           ***************987766555559*************7776667899*********************** PP

                             TIGR00761 129 eall..kagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeie 199
                                           eall  ++++ipv+a+++++ +g+++N+naDt+A++lA al+A+++++Ltd++G+l+g + +li+e+++e+++
  lcl|FitnessBrowser__Caulo:CCNA_00285 176 EALLtsEHDYIPVVAPIGVSPDGDTFNINADTVAGALAGALKAKRMLMLTDIKGVLDG-NGELIREMTIEQAR 247
                                           ***933468*************************************************.666*********** PP

                             TIGR00761 200 qlikqavikgGmipKveaalealesgvkkvvi 231
                                            li ++v++gGmipK+e+a++a+esgv++vvi
  lcl|FitnessBrowser__Caulo:CCNA_00285 248 ALIDTGVATGGMIPKLENAIHAIESGVEAVVI 279
                                           ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (304 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 7.52
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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