Alignments for a candidate for proB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Stenotrophomonas chelatiphaga DSM 21508

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_057687247.1 ABB28_RS15350 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_001431535.1:WP_057687247.1
          Length = 387

 Score =  269 bits (687), Expect = 1e-76
 Identities = 160/372 (43%), Positives = 224/372 (60%), Gaps = 10/372 (2%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           + D +  V+K+G+S+L      L+  H + L +  +    AG  +VIV+SGA+AAGR  L
Sbjct: 17  LPDWRRAVLKVGSSLLAADGGGLSPRHALGLAQFVSANVLAGREVVIVSSGAVAAGRAIL 76

Query: 61  GYPELP-ATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARD 119
              E   A +A++Q LAA+GQ++LI LW++ F      V Q+LLT  D+ +R R+LNAR 
Sbjct: 77  PRVEAAGAAMAARQALAALGQAQLIGLWQRFFER---PVAQVLLTHDDLRNRRRYLNARA 133

Query: 120 TLRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADP 179
           TL  LL    +PV+NEND V+  E+K+GDNDNL+A  A L  AD L + TD  GLY+ADP
Sbjct: 134 TLNELLRLGALPVVNENDTVSVDELKLGDNDNLAATVAALVDADVLFIATDIDGLYSADP 193

Query: 180 RSNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKP 239
           R +  A+ I  V  +   + A+AG S S  GTGGM TKL+AA  A R GI+TI+  G   
Sbjct: 194 RRDASAQPIPQVQELTADVLAMAGGSGSSAGTGGMRTKLEAASKAARLGIETILFNGRNG 253

Query: 240 GVIGDVMEGISVGTLFHAQATPLENRKRWIFGAP-PAGEITVDEGATAAILERGSSLLPK 298
            V+  + +G   GT  HA  +    RK W+  AP   G I +D+GA  A+  +G+SLLP 
Sbjct: 254 DVVRALAQGRLHGTRLHASQSREAARKYWLRHAPVEPGVIWIDDGAVQAMRGKGASLLPG 313

Query: 299 GIKSVTGNFSRGEVIRICNLEG-----RDIAHGVSRYNSDALRRIAGHHSQEIDAILGYE 353
           GI    G F RG+++ I    G       +A GV++Y +  +RRIAG HS++I+A LGY 
Sbjct: 314 GITGADGEFRRGDMVEIRCRPGAGGGEASVARGVTQYAASDIRRIAGRHSRDIEAALGYN 373

Query: 354 YGPVAVHRDDMI 365
           YG   VHRDD++
Sbjct: 374 YGGNVVHRDDLV 385


Lambda     K      H
   0.318    0.135    0.384 

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: 375
Number of extensions: 22
Number of successful extensions: 5
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: 367
Length of database: 387
Length adjustment: 30
Effective length of query: 337
Effective length of database: 357
Effective search space:   120309
Effective search space used:   120309
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: 50 (23.9 bits)

Align candidate WP_057687247.1 ABB28_RS15350 (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.18440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-124  401.4   0.1   2.2e-124  401.2   0.1    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057687247.1  ABB28_RS15350 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687247.1  ABB28_RS15350 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.2   0.1  2.2e-124  2.2e-124       2     362 ..      22     385 ..      21     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: 401.2 bits;  conditional E-value: 2.2e-124
                                 TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLg.lperpkklaekQ 69 
                                               r V+K+Gss+L+++ g l+  +   l++ v++   aG+evvivsSGavaaG + L  ++   + +a +Q
  lcl|NCBI__GCF_001431535.1:WP_057687247.1  22 RAVLKVGSSLLAADGGGLSPRHALGLAQFVSANVLAGREVVIVSSGAVAAGRAILPrVEAAGAAMAARQ 90 
                                               78*****************************************************725566799***** PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               alaa GQ++L+ l+++ f+   + vaQ+LLt++dl++r+rylNar+tl+ell lg++p+vNENDtv+v+
  lcl|NCBI__GCF_001431535.1:WP_057687247.1  91 ALAALGQAQLIGLWQRFFE---RPVAQVLLTHDDLRNRRRYLNARATLNELLRLGALPVVNENDTVSVD 156
                                               ***************9986...69********************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207
                                               e+k+GDND+L+a vaalv+Ad+L++ td+dgLy+adpr+++ A++i++v+e+++++ a+ag+sgss GT
  lcl|NCBI__GCF_001431535.1:WP_057687247.1 157 ELKLGDNDNLAATVAALVDADVLFIATDIDGLYSADPRRDASAQPIPQVQELTADVLAMAGGSGSSAGT 225
                                               ********************************************************************* PP

                                 TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276
                                               GGmrtKleaa+ A+r+g+e+i+ +g++ + + +l++++  gt ++a++++  +rk w+ +a+ + G i 
  lcl|NCBI__GCF_001431535.1:WP_057687247.1 226 GGMRTKLEAASKAARLGIETILFNGRNGDVVRALAQGRLHGTRLHASQSREAARKYWLRHAPVEPGVIW 294
                                               ********************************************************************* PP

                                 TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeeg.....qeigkglvnysseelekikglks 340
                                               +d+ga++a++ kg+sLlp g+++  g+F+rg++vei+ + g     +++++g+++y ++++++i+g++s
  lcl|NCBI__GCF_001431535.1:WP_057687247.1 295 IDDGAVQAMRGKGASLLPGGITGADGEFRRGDMVEIRCRPGagggeASVARGVTQYAASDIRRIAGRHS 363
                                               *************************************9877789999********************** PP

                                 TIGR01027 341 eeiedvLgyekkeevvhrdnlv 362
                                               ++ie+ Lgy++   vvhrd+lv
  lcl|NCBI__GCF_001431535.1:WP_057687247.1 364 RDIEAALGYNYGGNVVHRDDLV 385
                                               ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (387 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: 00:00:00.01
# Mc/sec: 10.94
//
[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