Alignments for a candidate for argB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Stenotrophomonas chelatiphaga DSM 21508

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_057687251.1 ABB28_RS15375 acetylglutamate kinase

Query= BRENDA::A0A0H2X8L7
         (447 letters)



>NCBI__GCF_001431535.1:WP_057687251.1
          Length = 442

 Score =  743 bits (1919), Expect = 0.0
 Identities = 382/447 (85%), Positives = 407/447 (91%), Gaps = 5/447 (1%)

Query: 1   MSLPAQPHKQTRQTIVRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDLEAL 60
           MS   QPH+QTRQTIVRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDLEAL
Sbjct: 1   MSPALQPHRQTRQTIVRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDLEAL 60

Query: 61  TSSLSFLQEVGLTPIVLHGAGPQLDAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQASN 120
           TSSLSFLQEVGLTPIVLHGAGPQLD EL+AAGIEKQTVNGLRVTSP ALAIVR+VFQ SN
Sbjct: 61  TSSLSFLQEVGLTPIVLHGAGPQLDTELAAAGIEKQTVNGLRVTSPEALAIVRQVFQQSN 120

Query: 121 LKLVEALQQNGARATSITGGVFEAEYLNRDTYGLVGEVKAVNLAPIEASLQAGSIPVITS 180
           L+LVEALQQNGARATSITGGVFEAEY+++ TYGLVGEVK VNLAPIEASL+AGSIPVITS
Sbjct: 121 LRLVEALQQNGARATSITGGVFEAEYMDQATYGLVGEVKKVNLAPIEASLRAGSIPVITS 180

Query: 181 LGETPSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGKLIDSINLSTEYDHLM 240
           LGET SGQILNVNADFAANELVQELQPYKIIFLTGTGGLLD EGK+IDSINLSTEY+HLM
Sbjct: 181 LGETRSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDEEGKVIDSINLSTEYEHLM 240

Query: 241 QQPWINGGMRVKIEQIKDLLDRLPLESSVSITRPADLAKELFTHKGSGTLVRRGERVLRA 300
            QPWI+GGM+VKIEQIK LLDRLPLESSVSITRPADLAKELFTHKGSGTLVR+GERVLRA
Sbjct: 241 TQPWIHGGMKVKIEQIKSLLDRLPLESSVSITRPADLAKELFTHKGSGTLVRKGERVLRA 300

Query: 301 TSWDELDLPRLTSLIESSFGRTLVPDYFSNTKLLRAYVSENYRAAVILTDEGMLGASALI 360
           TSWDELDLPRL  LIESSFGR LVPDYF  T+LLRAYVSENYR AVILTDE     +  +
Sbjct: 301 TSWDELDLPRLRGLIESSFGRVLVPDYFDKTRLLRAYVSENYRTAVILTDE-----AEGV 355

Query: 361 YLDKFAVLDDAQGEGLGRAVWNVMREETPQLFWRSRHNNQVNIFYYAESDGCIKQEKWKV 420
           YLDKFAVLDDAQGEGLGRAVWNVM +ETPQLFWRSR+ N +N FYYAESDGC KQ  WK 
Sbjct: 356 YLDKFAVLDDAQGEGLGRAVWNVMLDETPQLFWRSRNGNPINHFYYAESDGCYKQGTWKT 415

Query: 421 FWYGLENFEQIQHCVAHCATRQPTLLG 447
           FW+G + F++I+  V HCA R P+LLG
Sbjct: 416 FWFGADGFDRIKAYVDHCAQRAPSLLG 442


Lambda     K      H
   0.318    0.134    0.383 

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: 709
Number of extensions: 13
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: 447
Length of database: 442
Length adjustment: 32
Effective length of query: 415
Effective length of database: 410
Effective search space:   170150
Effective search space used:   170150
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: 51 (24.3 bits)

Align candidate WP_057687251.1 ABB28_RS15375 (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.20830.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.5e-67  212.0   0.2    5.9e-67  211.6   0.2    1.1  1  lcl|NCBI__GCF_001431535.1:WP_057687251.1  ABB28_RS15375 acetylglutamate ki


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687251.1  ABB28_RS15375 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.6   0.2   5.9e-67   5.9e-67       1     226 [.      43     264 ..      43     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 5.9e-67
                                 TIGR00761   1 tiViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlev 69 
                                               ++V+K+GGa++++ le+l + + +l+++g+ ++++HG gp+ ++ l + gie ++vnglRvT  e+l++
  lcl|NCBI__GCF_001431535.1:WP_057687251.1  43 FAVVKVGGAVLRDDLEALTSSLSFLQEVGLTPIVLHGAGPQLDTELAAAGIEKQTVNGLRVTSPEALAI 111
                                               58******************************************************************* PP

                                 TIGR00761  70 vemvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiip 138
                                               v++v+ +  n +lv++l+++g++a  +tg+   +++ae++d++++g+vGe+kkvn + +ea+l ag ip
  lcl|NCBI__GCF_001431535.1:WP_057687251.1 112 VRQVFQQ-SNLRLVEALQQNGARATSITGG---VFEAEYMDQATYGLVGEVKKVNLAPIEASLRAGSIP 176
                                               ****988.9********************9...************************************ PP

                                 TIGR00761 139 viaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliselel.eeieqlikqav 206
                                               vi+sl+ + +gq+lNvnaD aA el + l++ k+++Lt + G+l++ + ++i++++l  e+e+l++q +
  lcl|NCBI__GCF_001431535.1:WP_057687251.1 177 VITSLGETRSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDE-EGKVIDSINLsTEYEHLMTQPW 244
                                               **********************************************.666*******889********* PP

                                 TIGR00761 207 ikgGmipKveaalealesgv 226
                                               i+gGm+ K+e++++ l+ + 
  lcl|NCBI__GCF_001431535.1:WP_057687251.1 245 IHGGMKVKIEQIKSLLDRLP 264
                                               *************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (442 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: 11.25
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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