Alignments for a candidate for proB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate Echvi_4213 Echvi_4213 Glutamate 5-kinase

Query= curated2:Q1WRR5
         (267 letters)



>FitnessBrowser__Cola:Echvi_4213
          Length = 263

 Score =  135 bits (339), Expect = 1e-36
 Identities = 88/265 (33%), Positives = 148/265 (55%), Gaps = 10/265 (3%)

Query: 1   MENRNLQDAKRIVVKVGTSSLIRANGKINLQAIDELCYTLSGLVNEDKEVVLVSSGAVGV 60
           MEN + +  ++IVVKVG++ L     +I    +  L   L+ L  ++   +L++SG+V  
Sbjct: 1   MENLS-KKPRKIVVKVGSNMLTNHKNRIMDTVLQHLVGQLAELYEDNIMPILITSGSVAA 59

Query: 61  GLANMGLVQRPKQ-IPEQQALAAIGQSQLMTIYQQRFAMYSQKTSQILLTHDVLTYPESR 119
           G+  MG     K     +Q  +++GQ +LM  Y + F  Y  +  Q+L T    +  + R
Sbjct: 60  GMEAMGRELSIKDDAVRRQIYSSMGQPRLMRHYYEIFQQYGIRCGQVLATKRDFSPGKHR 119

Query: 120 ENVLNTFNELLKWKVIPVVNENDTVAVDEMDHQTSFGDNDWLSAVVASGIDADLLIVLSD 179
           EN++N +N L+   ++P+ NE+DTV++      ++F DND L+A+VA  ++AD+LI L+ 
Sbjct: 120 ENMINCYNGLIASGIVPIANEDDTVSLS----MSAFSDNDELAALVAELLEADMLIFLTH 175

Query: 180 IDGLFNKNPKKYADANLISEVTEINEKITGAAGGTG--SRFGTGGMATKIKAMDRMINEG 237
            DG+FN  P   A   ++ EV +I+EK        G     G G MA+K+K   +  ++ 
Sbjct: 176 KDGVFN-GPPDAAHTEVLEEV-KIDEKTEQYIHDKGDPKTIGRGNMASKLKMAKKAASKN 233

Query: 238 RKAVLANGKRPSIIFEILNGKQIGT 262
               +ANG  P+++ +I+NGKQIGT
Sbjct: 234 IAVHIANGTTPNVLLDIVNGKQIGT 258


Lambda     K      H
   0.315    0.133    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: 161
Number of extensions: 9
Number of successful extensions: 4
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: 267
Length of database: 263
Length adjustment: 25
Effective length of query: 242
Effective length of database: 238
Effective search space:    57596
Effective search space used:    57596
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 Echvi_4213 Echvi_4213 (Glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# 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/TIGR01027.hmm
# target sequence database:        /tmp/gapView.1914.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    3.1e-63  200.1   0.4    3.4e-63  199.9   0.4    1.0  1  lcl|FitnessBrowser__Cola:Echvi_4213  Echvi_4213 Glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4213  Echvi_4213 Glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.9   0.4   3.4e-63   3.4e-63       2     253 ..      10     262 ..       9     263 .] 0.94

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 3.4e-63
                            TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpk.klaekQalaaV 74 
                                          +iVvK+Gs++Lt++++++  + l++lv q+a+l ++    ++++SG+vaaG+ea+g +   k +   +Q+ ++ 
  lcl|FitnessBrowser__Cola:Echvi_4213  10 KIVVKVGSNMLTNHKNRIMDTVLQHLVGQLAELYEDNIMPILITSGSVAAGMEAMGRELSIKdDAVRRQIYSSM 83 
                                          8*******************************************************987655156789****** PP

                            TIGR01027  75 GQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtL 148
                                          GQ rLm++y ++f+qyg++ +Q+L t++d+s  ++ +N  n  + l++ g+vpi NE Dtv+ +   f DND+L
  lcl|FitnessBrowser__Cola:Echvi_4213  84 GQPRLMRHYYEIFQQYGIRCGQVLATKRDFSPGKHRENMINCYNGLIASGIVPIANEDDTVSLSMSAFSDNDEL 157
                                          ************************************************************************** PP

                            TIGR01027 149 salvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagss.gssvGTGGmrtKleaaelAs 221
                                          +alva l+eAd+L+ lt  dg+++  p   ++ +++eev+  e++ ++++ ++ ++++G G m++Kl+ a+ A+
  lcl|FitnessBrowser__Cola:Echvi_4213 158 AALVAELLEADMLIFLTHKDGVFNGPP-DAAHTEVLEEVKIDEKTEQYIHDKGdPKTIGRGNMASKLKMAKKAA 230
                                          ************************999.78888999998877777777776665788***************** PP

                            TIGR01027 222 ragveviiasgekpekiadlledaavgtlfea 253
                                          + ++ v ia+g++p+ ++d+++++++gt ++a
  lcl|FitnessBrowser__Cola:Echvi_4213 231 SKNIAVHIANGTTPNVLLDIVNGKQIGTRVMA 262
                                          ****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (263 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 0.00s 00:00:00.01 Elapsed: 00:00:00.03
# Mc/sec: 2.97
//
[ok]

This GapMind analysis is from Apr 09 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