Alignments for a candidate for proB in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Desulfarculus baarsii DSM 2075

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_013259203.1 DEBA_RS12000 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_000143965.1:WP_013259203.1
          Length = 388

 Score =  263 bits (673), Expect = 5e-75
 Identities = 150/365 (41%), Positives = 224/365 (61%), Gaps = 5/365 (1%)

Query: 4   SQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYP 63
           ++ +VVK+G+ VLTG  + L++  +  L  Q A+L AAG ++++V+SGAIA+GR  +G  
Sbjct: 10  ARRVVVKVGSGVLTG-PQGLDKRRVELLSGQLARLRAAGRQVLLVSSGAIASGRAKVGLA 68

Query: 64  ELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRA 123
            L  +I  KQ  AA+GQ+ L+Q +E     +G+   Q+LLT  D+  R+R+LNAR+T+  
Sbjct: 69  AL-RSIPEKQAAAALGQAGLMQTYEDALEAHGLLAAQILLTAGDLRSRQRYLNARNTINT 127

Query: 124 LLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNP 183
           LLD  ++P++NEND VA  EIK+GDNDNL+A+   L GA  ++ LT+  G+  ADPR+NP
Sbjct: 128 LLDWGVIPIVNENDTVAVDEIKLGDNDNLAAMLTNLLGASLMVNLTNVDGVLDADPRTNP 187

Query: 184 QAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIG 243
           QA+LI  V  +D AL   A      +G GG+ +K++AAD   R G  TI+A G    ++ 
Sbjct: 188 QAKLIPVVERVDAALLKAASTQPGAVGRGGIFSKVKAADKVARCGACTIVANGMVDDILD 247

Query: 244 DVMEGISVGTLFHAQATPLENRKRWI-FGA--PPAGEITVDEGATAAILERGSSLLPKGI 300
            +  G  +GT F A++ PL +RK WI F A     G I VD+GA A I   G SLL  G+
Sbjct: 248 RLFAGQELGTFFLARSHPLSSRKHWIAFTACQNQTGVIVVDQGAVAPISAGGKSLLAAGV 307

Query: 301 KSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVH 360
            +V G F  G  +++   +GR I  G+  Y+S  L +I G  S EI+  LG++     +H
Sbjct: 308 SAVRGRFGPGAAVKVIGPDGRTIGVGLCNYSSADLEKIKGLRSVEIEHSLGHKDFDEVIH 367

Query: 361 RDDMI 365
           RD+++
Sbjct: 368 RDNLV 372


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: 350
Number of extensions: 17
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: 367
Length of database: 388
Length adjustment: 30
Effective length of query: 337
Effective length of database: 358
Effective search space:   120646
Effective search space used:   120646
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_013259203.1 DEBA_RS12000 (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.4055581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-122  394.4   0.9     3e-122  394.2   0.9    1.0  1  NCBI__GCF_000143965.1:WP_013259203.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013259203.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.2   0.9    3e-122    3e-122       1     362 [.      11     372 ..      11     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: 394.2 bits;  conditional E-value: 3e-122
                             TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaa 73 
                                           +r+VvK+Gs +Lt ++g l++ +++ l  q+a+l++aG++v++vsSGa+a+G ++ gl    +++ ekQa+aa
  NCBI__GCF_000143965.1:WP_013259203.1  11 RRVVVKVGSGVLTGPQG-LDKRRVELLSGQLARLRAAGRQVLLVSSGAIASGRAKVGLAAL-RSIPEKQAAAA 81 
                                           59**************9.****************************************986.78********* PP

                             TIGR01027  74 VGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDND 146
                                            GQ+ Lm++ye++++ +gl  aQiLLt+ dl++r+rylNarnt+++ll++gv+pivNENDtvav+eik+GDND
  NCBI__GCF_000143965.1:WP_013259203.1  82 LGQAGLMQTYEDALEAHGLLAAQILLTAGDLRSRQRYLNARNTINTLLDWGVIPIVNENDTVAVDEIKLGDND 154
                                           ************************************************************************* PP

                             TIGR01027 147 tLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaael 219
                                           +L+a++++l++A l+v lt+vdg+ dadprtnp+Akli++ve+++++l + a++ + +vG GG+ +K++aa+ 
  NCBI__GCF_000143965.1:WP_013259203.1 155 NLAAMLTNLLGASLMVNLTNVDGVLDADPRTNPQAKLIPVVERVDAALLKAASTQPGAVGRGGIFSKVKAADK 227
                                           ****************************************************999999*************** PP

                             TIGR01027 220 Asragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaa..seakGkiivdegaeeallekgk 290
                                            +r+g  +i+a+g   + + +l +++++gt+f a+++ l++rk+wi+++  ++++G i+vd+ga++ +++ gk
  NCBI__GCF_000143965.1:WP_013259203.1 228 VARCGACTIVANGMVDDILDRLFAGQELGTFFLARSHPLSSRKHWIAFTacQNQTGVIVVDQGAVAPISAGGK 300
                                           **************9999999*************************987225789****************** PP

                             TIGR01027 291 sLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                           sLl+agv +v+g+F  g +v++  ++g++ig gl nyss++lekikgl+s eie+ Lg+++ +ev+hrdnlv
  NCBI__GCF_000143965.1:WP_013259203.1 301 SLLAAGVSAVRGRFGPGAAVKVIGPDGRTIGVGLCNYSSADLEKIKGLRSVEIEHSLGHKDFDEVIHRDNLV 372
                                           **********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (388 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: 00:00:00.00
# Mc/sec: 24.81
//
[ok]

This GapMind analysis is from Jul 25 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:

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 2024 update 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 original 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