Alignments for a candidate for proB in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Desulfovibrio vulgaris Miyazaki F

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 8500629 DvMF_1377 gamma-glutamyl kinase (RefSeq)

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__Miya:8500629
          Length = 395

 Score =  261 bits (668), Expect = 2e-74
 Identities = 150/369 (40%), Positives = 226/369 (61%), Gaps = 8/369 (2%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           ++D++ +VVK+G++VLT G   L+ A +  L  Q + +   G R+V+V+SGA+AAGR  L
Sbjct: 26  LADARCVVVKVGSAVLTNGEG-LDLAMVESLAGQLSAVQEGGRRVVLVSSGAVAAGRGVL 84

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
                 A +  +Q  +A+GQSRL+  +++ F+  G    Q+LLTR D++ R RFLNAR+T
Sbjct: 85  RSCCEIAGMPHRQAASAIGQSRLMHHYDEAFARCGRISAQVLLTRDDLKSRNRFLNARNT 144

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
             ALLD   +PV+NEND VA  ++K GDND L++L   +  AD  + +T   G++  +P+
Sbjct: 145 FAALLDWGAIPVVNENDTVAVHDLKFGDNDCLASLLLNIVEADLFVNMTSAGGVFAENPQ 204

Query: 181 SNPQA---ELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGS 237
            NP A     I DV+G+D  L  + G   S +GTGGM +KL +A  A + G+ T+I  G 
Sbjct: 205 DNPDACVMACIDDVHGLD--LNGLCGGKTS-VGTGGMYSKLLSARRAAQIGVPTLIVPGR 261

Query: 238 KPGVIGDVMEGISVGTLFHAQATPLENRKRWI-FGAPPAGEITVDEGATAAILERGSSLL 296
           +P V+  V  G ++GT   A A  +  RK W+ + + PAG +TVDEGA  A+L+ G SLL
Sbjct: 262 EPDVLARVFAGEAIGTWVRADARTVSRRKYWLAYQSDPAGTVTVDEGAARALLQGGKSLL 321

Query: 297 PKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGP 356
           P G+ +V G F  G ++R+   +G  I  G+S Y +  LRRI GH   E+ AILG  + P
Sbjct: 322 PGGVCAVEGGFGSGALVRVAAQDGTVIGVGLSNYAAAELRRIMGHKRHEVAAILGDAHYP 381

Query: 357 VAVHRDDMI 365
             +HRD+++
Sbjct: 382 EVIHRDNLL 390


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: 382
Number of extensions: 20
Number of successful extensions: 5
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: 395
Length adjustment: 30
Effective length of query: 337
Effective length of database: 365
Effective search space:   123005
Effective search space used:   123005
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 8500629 DvMF_1377 (gamma-glutamyl kinase (RefSeq))
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.2071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.4e-119  382.9   0.0   9.7e-119  382.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8500629  DvMF_1377 gamma-glutamyl kinase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500629  DvMF_1377 gamma-glutamyl kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.7   0.0  9.7e-119  9.7e-119       3     362 ..      32     390 ..      30     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 382.7 bits;  conditional E-value: 9.7e-119
                         TIGR01027   3 iVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgrL 79 
                                       +VvK+Gs++Lt+++g l+++++++l+ q++++++ G++vv+vsSGavaaG   L      + + ++Qa++a+GQ+rL
  lcl|FitnessBrowser__Miya:8500629  32 VVVKVGSAVLTNGEG-LDLAMVESLAGQLSAVQEGGRRVVLVSSGAVAAGRGVLRSCCEIAGMPHRQAASAIGQSRL 107
                                       9*************9.************************************************************* PP

                         TIGR01027  80 mklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalv 156
                                       m++y+++f++ g+ +aQ+LLtr+dl++r+r+lNarnt+ +ll++g++p+vNENDtvav+++kfGDND L+ l+ ++v
  lcl|FitnessBrowser__Miya:8500629 108 MHHYDEAFARCGRISAQVLLTRDDLKSRNRFLNARNTFAALLDWGAIPVVNENDTVAVHDLKFGDNDCLASLLLNIV 184
                                       ***************************************************************************** PP

                         TIGR01027 157 eAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasge 233
                                       eAdl v +t++ g++ ++p+ npdA ++  +++++    +   ++ +svGTGGm +Kl +a+ A++ gv+++i++g+
  lcl|FitnessBrowser__Miya:8500629 185 EADLFVNMTSAGGVFAENPQDNPDACVMACIDDVHGLDLNGLCGGKTSVGTGGMYSKLLSARRAAQIGVPTLIVPGR 261
                                       **********************************99888877777899***************************** PP

                         TIGR01027 234 kpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevv 310
                                       +p+ +a++ +++a+gt + a +++++ rk w++++s+++G+++vdega++all+ gksLlp gv +veg F +g  v
  lcl|FitnessBrowser__Miya:8500629 262 EPDVLARVFAGEAIGTWVRADARTVSRRKYWLAYQSDPAGTVTVDEGAARALLQGGKSLLPGGVCAVEGGFGSGALV 338
                                       ***************************************************************************** PP

                         TIGR01027 311 eilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                       ++ a++g+ ig gl+ny ++el++i+g+k +e++++Lg  +  ev+hrdnl+
  lcl|FitnessBrowser__Miya:8500629 339 RVAAQDGTVIGVGLSNYAAAELRRIMGHKRHEVAAILGDAHYPEVIHRDNLL 390
                                       **************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (395 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: 00:00:00.01
# Mc/sec: 12.03
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code, or see 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