GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Caldicellulosiruptor kronotskyensis 2002

Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate WP_013430064.1 CALKRO_RS05445 glutamate 5-kinase

Query= curated2:Q8XHA6
         (269 letters)



>NCBI__GCF_000166775.1:WP_013430064.1
          Length = 266

 Score =  297 bits (761), Expect = 1e-85
 Identities = 151/260 (58%), Positives = 200/260 (76%), Gaps = 4/260 (1%)

Query: 7   DSKRIVVKVGTSTLTYENGSVNLMRIEKLSRVISDICNMGKEVVLVSSGAIGVGVGKLRL 66
           ++K+IVVKVGTST+TY  G +NL R+EKL+RV+SDI N G++VVLV+SGA+  G+G+L L
Sbjct: 6   NAKKIVVKVGTSTVTYPTGKLNLSRLEKLARVLSDIKNEGRDVVLVTSGAVASGLGRLGL 65

Query: 67  EKKPETIREKQAVAAVGQCALMHIYNKFFGEYSHVVAQVLLTRDVLENERMKNNVCNTFD 126
            K  +T +EKQA+AA+GQ  LM IY K FGEY  VVAQVLLT+DV++ E+   NV NTF+
Sbjct: 66  TKNHKTTQEKQALAAIGQGILMQIYEKLFGEYGVVVAQVLLTKDVVDEEKKMLNVKNTFE 125

Query: 127 TLLEKGIIPIVNENDAISIDEIQNILNFGDNDNLSAIVSTLVNADTLIILSDIDGFYDSD 186
            L + G IPIVNEND ++I+E    L FGDND LSA V+T++ AD LIILSDIDG Y  D
Sbjct: 126 YLFKYGAIPIVNENDVVAIEE----LEFGDNDTLSAYVATIIGADLLIILSDIDGLYSCD 181

Query: 187 PRTNEDSKMLKEVYEITPEIEECAGGAGSNRGTGGMVTKLSAAKVATSNGIDMILANGEN 246
           PR ++ ++++KEV+EI   IE  AGGAG+   TGGM TK+ AAK+A  +GI M++ANGEN
Sbjct: 182 PRIDKSAELIKEVFEIDSYIESIAGGAGTLNSTGGMQTKIEAAKIAMQHGIPMVIANGEN 241

Query: 247 PEILIDILNGEDIGTMFVAK 266
           P I+ +IL G++IGT+FV+K
Sbjct: 242 PSIVKEILEGKEIGTLFVSK 261


Lambda     K      H
   0.315    0.134    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: 234
Number of extensions: 7
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: 269
Length of database: 266
Length adjustment: 25
Effective length of query: 244
Effective length of database: 241
Effective search space:    58804
Effective search space used:    58804
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

Align candidate WP_013430064.1 CALKRO_RS05445 (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.859179.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    5.1e-98  314.5   3.2    5.6e-98  314.3   3.2    1.0  1  NCBI__GCF_000166775.1:WP_013430064.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430064.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.3   3.2   5.6e-98   5.6e-98       1     255 [.       8     262 ..       8     266 .] 0.99

  Alignments for each domain:
  == domain 1  score: 314.3 bits;  conditional E-value: 5.6e-98
                             TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaa 73 
                                           k+iVvK+G+s++t ++gkl++s+l++l++ ++ +k++G++vv+v+SGava+Gl +Lgl++  k+ +ekQalaa
  NCBI__GCF_000166775.1:WP_013430064.1   8 KKIVVKVGTSTVTYPTGKLNLSRLEKLARVLSDIKNEGRDVVLVTSGAVASGLGRLGLTKNHKTTQEKQALAA 80 
                                           68*********************************************************************** PP

                             TIGR01027  74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDND 146
                                           +GQg Lm+ yeklf +yg  vaQ+LLt++ + ++++ lN +nt+e l++ g++pivNEND va+ee++fGDND
  NCBI__GCF_000166775.1:WP_013430064.1  81 IGQGILMQIYEKLFGEYGVVVAQVLLTKDVVDEEKKMLNVKNTFEYLFKYGAIPIVNENDVVAIEELEFGDND 153
                                           ************************************************************************* PP

                             TIGR01027 147 tLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaael 219
                                           tLsa+va++++AdlL++l+d+dgLy++dpr +  A+li+ev ei++ ++++ag++g+ + TGGm+tK+eaa++
  NCBI__GCF_000166775.1:WP_013430064.1 154 TLSAYVATIIGADLLIILSDIDGLYSCDPRIDKSAELIKEVFEIDSYIESIAGGAGTLNSTGGMQTKIEAAKI 226
                                           ************************************************************************* PP

                             TIGR01027 220 Asragveviiasgekpekiadlledaavgtlfeakk 255
                                           A++ g++++ia+ge+p+ + ++le++++gtlf +k+
  NCBI__GCF_000166775.1:WP_013430064.1 227 AMQHGIPMVIANGENPSIVKEILEGKEIGTLFVSKN 262
                                           ********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (266 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: 00:00:00.00
# Mc/sec: 19.63
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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