Alignments for a candidate for proB in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Nocardiopsis lucentensis DSM 44048

Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate WP_017597788.1 D471_RS0105990 glutamate 5-kinase

Query= curated2:Q82C83
         (375 letters)



>NCBI__GCF_000341125.1:WP_017597788.1
          Length = 292

 Score =  335 bits (860), Expect = 7e-97
 Identities = 180/279 (64%), Positives = 212/279 (75%), Gaps = 2/279 (0%)

Query: 3   AARQGVAQARRIVVKVGSSSLTTAAGGLDADRVDALVDVLAKSRSGGEKEIVLVSSGAIA 62
           A R+ VA ARR+VVKVGSSSLTT  G +D+ R+  LV+VLA  R+ G+ E++LVSSGA+A
Sbjct: 15  AGRKAVANARRVVVKVGSSSLTTPEGRIDSSRIRDLVEVLAARRALGQ-EVILVSSGAVA 73

Query: 63  AGLAPLGLRRRPKDLARQQAAASVGQGLLVARYTASCARHGIRVGQVLLTSDDTSRRAHH 122
           AG+ PLGL RRP+DLA QQAAASVGQGLL+A YTA  A HG+   QVLLT +D  RR  H
Sbjct: 74  AGMTPLGLTRRPRDLASQQAAASVGQGLLLASYTAELAGHGLTAAQVLLTVEDMMRRVQH 133

Query: 123 RNASRTLDKLLAMGALPVVNENDTVATDEIRFGDNDRLAALVAHLVRADLLVLLSDVDGV 182
           RNA RTL +LL +GA+P+VNENDTVAT EIRFGDNDRLAALVAHL+RAD LVLLSDVD +
Sbjct: 134 RNAQRTLRRLLDIGAVPIVNENDTVATHEIRFGDNDRLAALVAHLLRADALVLLSDVDAL 193

Query: 183 YDGDPSKPGTSRVAQVHGPQDLAHVEIGSAGRAGVGTGGMVTKIEAARIAAAAGIPVVLT 242
           YDG+PS P TS V  V GP DL  ++IG AG+ GVGTGGMVTK+E+ARIA  AG+  VLT
Sbjct: 194 YDGNPSDPSTSVVDLVRGPGDLDGIDIGGAGKRGVGTGGMVTKVESARIATEAGVQTVLT 253

Query: 243 SAVHAADALAGRDTGTYFHPT-GKRSADRLLWLQHASTP 280
           SA +A  ALAG   GT F P  G+R + R LWL     P
Sbjct: 254 SAANARAALAGERVGTLFAPAEGRRPSTRQLWLPPPPPP 292


Lambda     K      H
   0.317    0.133    0.369 

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: 247
Number of extensions: 3
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: 375
Length of database: 292
Length adjustment: 28
Effective length of query: 347
Effective length of database: 264
Effective search space:    91608
Effective search space used:    91608
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: 49 (23.5 bits)

Align candidate WP_017597788.1 D471_RS0105990 (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.28283.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.9e-98  314.5   0.0    5.9e-98  314.3   0.0    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017597788.1  D471_RS0105990 glutamate 5-kinas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017597788.1  D471_RS0105990 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.3   0.0   5.9e-98   5.9e-98       1     265 [.      24     286 ..      24     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 314.3 bits;  conditional E-value: 5.9e-98
                                 TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 
                                               +r+VvK+GsssLt+++g++++s++++lve +a++++ G+ev++vsSGavaaG++ Lgl++rp++la++Q
  lcl|NCBI__GCF_000341125.1:WP_017597788.1  24 RRVVVKVGSSSLTTPEGRIDSSRIRDLVEVLAARRALGQEVILVSSGAVAAGMTPLGLTRRPRDLASQQ 92 
                                               59******************************************************************* PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               a+a+VGQg L+++y++ ++ +gl+ aQ+LLt +d+ +r +++Na++tl++ll++g+vpivNENDtva++
  lcl|NCBI__GCF_000341125.1:WP_017597788.1  93 AAASVGQGLLLASYTAELAGHGLTAAQVLLTVEDMMRRVQHRNAQRTLRRLLDIGAVPIVNENDTVATH 161
                                               ********************************************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgss.vG 206
                                               ei+fGDND+L+alva+l+ Ad+Lvll+dvd+Lyd +p ++p   +++ v+   +      g++g++ vG
  lcl|NCBI__GCF_000341125.1:WP_017597788.1 162 EIRFGDNDRLAALVAHLLRADALVLLSDVDALYDGNP-SDPSTSVVDLVRGPGDLDGIDIGGAGKRgVG 229
                                               *************************************.**************999998888888877** PP

                                 TIGR01027 207 TGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeak.kkklknrkqwi 265
                                               TGGm tK+e+a++A++agv+++++s+++     ++l+++ vgtlf++   ++ ++r+ w+
  lcl|NCBI__GCF_000341125.1:WP_017597788.1 230 TGGMVTKVESARIATEAGVQTVLTSAAN---ARAALAGERVGTLFAPAeGRRPSTRQLWL 286
                                               *************************996...8899***********99667799999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (292 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: 00:00:00.01
# Mc/sec: 6.98
//
[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