Alignments for a candidate for proB in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Thiomicrorhabdus chilensis DSM 12352

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_028487247.1 B076_RS0110330 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_000483485.1:WP_028487247.1
          Length = 374

 Score =  279 bits (714), Expect = 8e-80
 Identities = 149/366 (40%), Positives = 223/366 (60%), Gaps = 1/366 (0%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           +  S+  V+K+G+++LT   + LN A + + V+Q  +L   G  +VIV+SG++A G + L
Sbjct: 6   LKQSKRWVIKIGSALLTNDGQGLNLAELKKWVKQMVRLREQGVEVVIVSSGSVAEGMQRL 65

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
           G+   P+ +   Q  AAVGQ  L+Q +E  F+ Y I   Q+L+T  D+ +R+R+LN + T
Sbjct: 66  GWKTRPSALHELQAAAAVGQMGLVQAYESEFAHYDIRTAQILMTHDDLSNRKRYLNVKST 125

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           L+ LL   ++PVINEND V T EI+ GDND L+AL A L GAD L++LTDQ+GLY  +PR
Sbjct: 126 LQTLLSYGVIPVINENDTVVTDEIRFGDNDTLAALTANLIGADVLVILTDQQGLYDDNPR 185

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
            NP A+LI         + A+A  +   LG GGM TK+ AA  A R+G  T+IA+G +  
Sbjct: 186 ENPNAKLIGKAQVSRKDIEAMASPTGGALGKGGMYTKVMAAKRAARSGTATLIASGREAD 245

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFGAPPA-GEITVDEGATAAILERGSSLLPKG 299
           ++  +  G   GTL      PL  R++W+ G   A G++ +D+GA A +   G SLLP G
Sbjct: 246 ILPRLFAGEQQGTLLVPDLEPLTARQQWLAGHLQAKGKVVLDDGAVAMLQNSGKSLLPIG 305

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +KSV G F RGE++   N  G+++A G+  Y     ++I G  S +I+AILGY      +
Sbjct: 306 VKSVEGRFQRGEMVVCFNQAGQEVARGLINYPIHEAQKIVGQPSHQIEAILGYVDEESLI 365

Query: 360 HRDDMI 365
           HRD+++
Sbjct: 366 HRDNLV 371


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: 334
Number of extensions: 14
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: 367
Length of database: 374
Length adjustment: 30
Effective length of query: 337
Effective length of database: 344
Effective search space:   115928
Effective search space used:   115928
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_028487247.1 B076_RS0110330 (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.16862.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-133  431.6   1.4   1.4e-133  431.4   1.4    1.0  1  lcl|NCBI__GCF_000483485.1:WP_028487247.1  B076_RS0110330 glutamate 5-kinas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000483485.1:WP_028487247.1  B076_RS0110330 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.4   1.4  1.4e-133  1.4e-133       2     362 ..      11     371 ..      10     372 .. 0.99

  Alignments for each domain:
  == domain 1  score: 431.4 bits;  conditional E-value: 1.4e-133
                                 TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQa 70 
                                               r V+K+Gs++Lt++ + l++++l++ v+q+ +l+++G evvivsSG+va G+++Lg ++rp  l+e Qa
  lcl|NCBI__GCF_000483485.1:WP_028487247.1  11 RWVIKIGSALLTNDGQGLNLAELKKWVKQMVRLREQGVEVVIVSSGSVAEGMQRLGWKTRPSALHELQA 79 
                                               78******************************************************************* PP

                                 TIGR01027  71 laaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvavee 139
                                               +aaVGQ  L+++ye+ f++y++++aQiL+t++dls+r+rylN ++tl++ll+ gv+p++NENDtv ++e
  lcl|NCBI__GCF_000483485.1:WP_028487247.1  80 AAAVGQMGLVQAYESEFAHYDIRTAQILMTHDDLSNRKRYLNVKSTLQTLLSYGVIPVINENDTVVTDE 148
                                               ********************************************************************* PP

                                 TIGR01027 140 ikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTG 208
                                               i+fGDNDtL+al+a+l++Ad+Lv+ltd++gLyd++pr+np+Akli + +  +++++a+a+ +g ++G G
  lcl|NCBI__GCF_000483485.1:WP_028487247.1 149 IRFGDNDTLAALTANLIGADVLVILTDQQGLYDDNPRENPNAKLIGKAQVSRKDIEAMASPTGGALGKG 217
                                               ********************************************************************* PP

                                 TIGR01027 209 GmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiiv 277
                                               Gm tK+ aa+ A+r+g  ++iasg++ + + +l ++++ gtl+ +  + l +r+qw++ +++akGk+++
  lcl|NCBI__GCF_000483485.1:WP_028487247.1 218 GMYTKVMAAKRAARSGTATLIASGREADILPRLFAGEQQGTLLVPDLEPLTARQQWLAGHLQAKGKVVL 286
                                               ********************************************************************* PP

                                 TIGR01027 278 degaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedv 346
                                               d+ga++ l++ gksLlp gv +veg+F+rge+v + +++gqe+++gl ny  +e +ki+g++s++ie++
  lcl|NCBI__GCF_000483485.1:WP_028487247.1 287 DDGAVAMLQNSGKSLLPIGVKSVEGRFQRGEMVVCFNQAGQEVARGLINYPIHEAQKIVGQPSHQIEAI 355
                                               ********************************************************************* PP

                                 TIGR01027 347 Lgyekkeevvhrdnlv 362
                                               Lgy ++e  +hrdnlv
  lcl|NCBI__GCF_000483485.1:WP_028487247.1 356 LGYVDEESLIHRDNLV 371
                                               **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (374 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.19
//
[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