Alignments for a candidate for proB in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Dechlorosoma suillum PS

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate Dsui_0166 Dsui_0166 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__PS:Dsui_0166
          Length = 377

 Score =  307 bits (787), Expect = 3e-88
 Identities = 168/360 (46%), Positives = 231/360 (64%), Gaps = 2/360 (0%)

Query: 7   LVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELP 66
           LVVK+G++++T     L+ A I E  RQ A+L   G ++V+V+SGAIA G + LG+ + P
Sbjct: 14  LVVKVGSALVTNNGAGLDLAAIHEWARQIAELRHNGKQVVLVSSGAIACGMQRLGWQKRP 73

Query: 67  ATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLD 126
             +   Q  AAVGQ  L Q++E  FS +G+H  Q+LLT  D+ DR+R+LNAR TL  LL+
Sbjct: 74  KAVHELQAAAAVGQMGLAQVYESAFSAHGLHTAQILLTHDDLADRKRYLNARATLTTLLE 133

Query: 127 NNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAE 186
             +VP+INEND V T EIK GDND L AL A L  AD L++LTDQ GL+TADPR +P A 
Sbjct: 134 LGVVPIINENDTVVTDEIKFGDNDTLGALVANLVEADCLIILTDQPGLFTADPRKDPSAT 193

Query: 187 LIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVM 246
           LI      D +L A+AG + + +GTGGM TK+ AA  A R+G DT+IA+G +   +  + 
Sbjct: 194 LITSARAGDPSLEAMAGGAGTQIGTGGMITKVLAAKRAARSGADTVIASGREKSPLTRLA 253

Query: 247 EGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKGIKSVTG 305
            G SVGTL  A   P+  RK+W+      AG++T+D+GA  A L +G SLLP G++ V G
Sbjct: 254 TGESVGTLLVADTLPMTARKQWLADHLQLAGKLTLDQGAIQA-LRQGKSLLPVGVREVHG 312

Query: 306 NFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365
           +F RG  +   +  GR+IA G+  Y S  +R IA H S +I+ ILGY   P  +HRD+M+
Sbjct: 313 DFERGAAVACLDESGREIARGLCNYGSSEVRLIAKHSSSDIEDILGYMEEPELIHRDNMV 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: 366
Number of extensions: 15
Number of successful extensions: 3
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: 377
Length adjustment: 30
Effective length of query: 337
Effective length of database: 347
Effective search space:   116939
Effective search space used:   116939
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 Dsui_0166 Dsui_0166 (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.18774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.9e-137  443.6   0.5   3.3e-137  443.4   0.5    1.0  1  lcl|FitnessBrowser__PS:Dsui_0166  Dsui_0166 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0166  Dsui_0166 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.4   0.5  3.3e-137  3.3e-137       2     362 ..      13     372 ..      12     373 .. 0.99

  Alignments for each domain:
  == domain 1  score: 443.4 bits;  conditional E-value: 3.3e-137
                         TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgr 78 
                                       r+VvK+Gs+++t++   l+++ ++e ++q+a+l+++G++vv+vsSGa+a G+++Lg ++rpk ++e Qa+aaVGQ  
  lcl|FitnessBrowser__PS:Dsui_0166  13 RLVVKVGSALVTNNGAGLDLAAIHEWARQIAELRHNGKQVVLVSSGAIACGMQRLGWQKRPKAVHELQAAAAVGQMG 89 
                                       79************999************************************************************ PP

                         TIGR01027  79 LmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaal 155
                                       L + ye++fs +gl++aQiLLt++dl++r+rylNar+tl++llelgvvpi+NENDtv ++eikfGDNDtL alva+l
  lcl|FitnessBrowser__PS:Dsui_0166  90 LAQVYESAFSAHGLHTAQILLTHDDLADRKRYLNARATLTTLLELGVVPIINENDTVVTDEIKFGDNDTLGALVANL 166
                                       ***************************************************************************** PP

                         TIGR01027 156 veAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasg 232
                                       veAd L++ltd+ gL++adpr++p A+li   ++ + +l+a+ag++g+++GTGGm tK+ aa+ A+r+g +++iasg
  lcl|FitnessBrowser__PS:Dsui_0166 167 VEADCLIILTDQPGLFTADPRKDPSATLITSARAGDPSLEAMAGGAGTQIGTGGMITKVLAAKRAARSGADTVIASG 243
                                       ***************************************************************************** PP

                         TIGR01027 233 ekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgev 309
                                       ++++ +++l+ +++vgtl+ a +  + +rkqw++ +++ +Gk+++d+ga +al++ gksLlp+gv ev+g+F+rg +
  lcl|FitnessBrowser__PS:Dsui_0166 244 REKSPLTRLATGESVGTLLVADTLPMTARKQWLADHLQLAGKLTLDQGAIQALRQ-GKSLLPVGVREVHGDFERGAA 319
                                       *****************************************************98.********************* PP

                         TIGR01027 310 veilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                       v +l+e+g+ei++gl ny s+e++ i++++s++ied+Lgy ++ e +hrdn+v
  lcl|FitnessBrowser__PS:Dsui_0166 320 VACLDESGREIARGLCNYGSSEVRLIAKHSSSDIEDILGYMEEPELIHRDNMV 372
                                       ***************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (377 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: 11.43
//
[ok]

This GapMind analysis is from Apr 09 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