Alignments for a candidate for proB in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Shewanella loihica PV-4

Align Glutamate 5-kinase 1; EC 2.7.2.11; Gamma-glutamyl kinase 1; GK 1 (uncharacterized)
to candidate 5210586 Shew_3014 gamma-glutamyl kinase (RefSeq)

Query= curated2:Q3IEY8
         (368 letters)



>FitnessBrowser__PV4:5210586
          Length = 366

 Score =  481 bits (1238), Expect = e-140
 Identities = 233/366 (63%), Positives = 293/366 (80%)

Query: 1   MNKLNWRRIVLKVGSALIAPDQDGCRSRYILTIAQFIVRCRARGIEVILVSSGSVAAGAH 60
           M  ++W+RIV+KVGSALIAP + GC S Y+L IAQFI  CRA+G++V+LVSSGSVAAG H
Sbjct: 1   MANIHWKRIVVKVGSALIAPHKQGCSSHYLLGIAQFIANCRAQGVQVVLVSSGSVAAGWH 60

Query: 61  LFPSDTARSVVMKKAMAAAGQTEMIAMWDRFFDFPSAQLLLTHGDLRDHERYQSIRETVF 120
                   SV  KKAMAAAGQ +M+A WD+ FDFPSAQLL+THGDLRD ERY SI+ T+F
Sbjct: 61  RLGDVKQPSVSQKKAMAAAGQADMMATWDKLFDFPSAQLLVTHGDLRDRERYISIKNTLF 120

Query: 121 TLLEHGVLPIINENDAVTTDDLKVGDNDNLSAMVAAAADADALLIFSDVDGLYDKNPNLH 180
           +LL+HG+LPI+NENDAVTTD L+VGDNDNLSAMVAAAADADAL+I SDV+GLY KNP LH
Sbjct: 121 SLLDHGLLPIVNENDAVTTDTLRVGDNDNLSAMVAAAADADALIICSDVNGLYTKNPQLH 180

Query: 181 DDAILLPEIKSIDDSIYAMAGCATSAVGTGGMKTKIEAAEKATSHGISTYIINGFKEETF 240
           DDA L+ ++  I+++IYAMAG ATS VGTGGM+TKIEAAEKA +HGI T IINGF  + F
Sbjct: 181 DDAKLIKQVNEINEAIYAMAGGATSEVGTGGMRTKIEAAEKAIAHGIETVIINGFDPDAF 240

Query: 241 TRLLAGENPGTIFLPYEKPMQDSVHWMTHTANEQGEVVVDGSFDKSLEGETGCIRGDEIM 300
            RLL G+NPGT+F P+++PMQ+ VHWMTHT+  QGEV+V+ +FD  L+ +   +  D+++
Sbjct: 241 NRLLKGQNPGTLFTPFDQPMQEHVHWMTHTSQAQGEVIVEDNFDAPLDDQETQLTSDDVV 300

Query: 301 AVHGEFAIGDTILVRSEDGTRLAKATANYSSCLLSFIADNEQSEFSEKMQDSIGPVISEK 360
           AV G F++GDTILVR  DGT+LAKA ANYSSCLLSFIA      F+  ++   GP++S++
Sbjct: 301 AVKGNFSVGDTILVRKGDGTKLAKAQANYSSCLLSFIAKQPDRAFAHDVEQQTGPILSDE 360

Query: 361 HIALLE 366
           +IA+LE
Sbjct: 361 NIAILE 366


Lambda     K      H
   0.318    0.133    0.382 

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: 435
Number of extensions: 15
Number of successful extensions: 1
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: 368
Length of database: 366
Length adjustment: 30
Effective length of query: 338
Effective length of database: 336
Effective search space:   113568
Effective search space used:   113568
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 5210586 Shew_3014 (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.23578.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
     2e-103  332.3   0.7   2.3e-103  332.0   0.7    1.0  1  lcl|FitnessBrowser__PV4:5210586  Shew_3014 gamma-glutamyl kinase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210586  Shew_3014 gamma-glutamyl kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.0   0.7  2.3e-103  2.3e-103       1     343 [.       7     345 ..       7     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 332.0 bits;  conditional E-value: 2.3e-103
                        TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgr 78 
                                      kriVvK+Gs++++ +++  ++++l  +++ +a+ +++G +vv+vsSG+vaaG+++Lg  ++p ++++k a+aa GQ+ 
  lcl|FitnessBrowser__PV4:5210586   7 KRIVVKVGSALIAPHKQGCSSHYLLGIAQFIANCRAQGVQVVLVSSGSVAAGWHRLGDVKQP-SVSQKKAMAAAGQAD 83 
                                      69*******************************************************98887.699************ PP

                        TIGR01027  79 LmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalv 156
                                      +m++++klf+     +aQ+L t+ dl++rery   +ntl +ll+ g +pivNEND+v+++ +++GDND+Lsa+vaa  
  lcl|FitnessBrowser__PV4:5210586  84 MMATWDKLFD---FPSAQLLVTHGDLRDRERYISIKNTLFSLLDHGLLPIVNENDAVTTDTLRVGDNDNLSAMVAAAA 158
                                      ********97...589************************************************************** PP

                        TIGR01027 157 eAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasgek 234
                                      +Ad+L++ +dv+gLy+++p+ + dAkli++v+ei+e++ a+ag+++s+vGTGGmrtK+eaae A + g+e++i++g +
  lcl|FitnessBrowser__PV4:5210586 159 DADALIICSDVNGLYTKNPQLHDDAKLIKQVNEINEAIYAMAGGATSEVGTGGMRTKIEAAEKAIAHGIETVIINGFD 236
                                      ****************************************************************************** PP

                        TIGR01027 235 pekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevvei 312
                                      p++  +ll++++ gtlf++ ++ ++++ +w++++s+a+G++iv+++  + l ++++ L+   vv+v+gnFs g+++ +
  lcl|FitnessBrowser__PV4:5210586 237 PDAFNRLLKGQNPGTLFTPFDQPMQEHVHWMTHTSQAQGEVIVEDNFDAPLDDQETQLTSDDVVAVKGNFSVGDTILV 314
                                      ****************************************************************************** PP

                        TIGR01027 313 laeegqeigkglvnysseelekikglkseei 343
                                      ++ +g++++k+++nyss  l+ i++++ +  
  lcl|FitnessBrowser__PV4:5210586 315 RKGDGTKLAKAQANYSSCLLSFIAKQPDRAF 345
                                      ********************99999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (366 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.11
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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
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