Alignments for a candidate for proB in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Marinobacter adhaerens HP15

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate GFF520 HP15_508 gamma-glutamyl kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__Marino:GFF520
          Length = 374

 Score =  286 bits (733), Expect = 5e-82
 Identities = 157/366 (42%), Positives = 221/366 (60%), Gaps = 1/366 (0%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           +  ++ LV+K+G+++LT   R L+ A +   V Q A+L   G  +V+V+SG++A G   L
Sbjct: 7   LRQARRLVIKIGSALLTNDGRGLDVAALGLWVDQIAELIEDGVEVVVVSSGSVAEGMSRL 66

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
           G+   P  +   Q  AAVGQ  L+Q WE  F  + IH  Q+LLT  D+ DR+R+LN R T
Sbjct: 67  GWTVRPEQLHELQAAAAVGQMGLVQTWEAQFKRHDIHTAQILLTHDDLSDRKRYLNGRGT 126

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           LRALL+  +VP++NEND V T EI+ GDND L AL A L  AD L++LTDQ GL+  DPR
Sbjct: 127 LRALLNLGVVPIVNENDTVVTDEIRFGDNDTLGALVANLIEADGLIILTDQLGLFDKDPR 186

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
            +  A L+ +    D  L A+AG     LG GGM TKL+AA +A R+G  T+I  G   G
Sbjct: 187 KHSDACLVTERRAGDRELDAMAGGGAGVLGRGGMQTKLRAARLAARSGAFTVIVGGRIEG 246

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299
           VIG + +G  +GTL   +   +  RK+W+       G +T+D+GA   +   G SLLP G
Sbjct: 247 VIGRLRQGDVIGTLLLPEQGRIAARKQWLASHLQTRGRLTLDDGAVKVLCLGGRSLLPVG 306

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +K V+G F RGE++   +  GR+IA G+  Y++D  R IAG  S  I  ILGY  G   +
Sbjct: 307 VKGVSGQFRRGEMVSCFDQSGREIARGLVNYDADEARAIAGRSSDRITEILGYMSGEEMI 366

Query: 360 HRDDMI 365
           HRD+++
Sbjct: 367 HRDNLV 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: 382
Number of extensions: 17
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 GFF520 HP15_508 (gamma-glutamyl 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.6143.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-129  418.3   0.2   1.7e-129  418.1   0.2    1.0  1  lcl|FitnessBrowser__Marino:GFF520  HP15_508 gamma-glutamyl kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF520  HP15_508 gamma-glutamyl kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.1   0.2  1.7e-129  1.7e-129       1     363 []      11     373 ..      11     373 .. 0.99

  Alignments for each domain:
  == domain 1  score: 418.1 bits;  conditional E-value: 1.7e-129
                          TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQ 76 
                                        +r+V+K+Gs++Lt++ + l+ + l   v q+a+l ++G evv+vsSG+va G+++Lg + rp++l+e Qa+aaVGQ
  lcl|FitnessBrowser__Marino:GFF520  11 RRLVIKIGSALLTNDGRGLDVAALGLWVDQIAELIEDGVEVVVVSSGSVAEGMSRLGWTVRPEQLHELQAAAAVGQ 86 
                                        589************************************************************************* PP

                          TIGR01027  77 grLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalv 152
                                          L++++e++f+++++++aQiLLt++dls+r+rylN r tl++ll+lgvvpivNENDtv ++ei+fGDNDtL alv
  lcl|FitnessBrowser__Marino:GFF520  87 MGLVQTWEAQFKRHDIHTAQILLTHDDLSDRKRYLNGRGTLRALLNLGVVPIVNENDTVVTDEIRFGDNDTLGALV 162
                                        **************************************************************************** PP

                          TIGR01027 153 aalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragvevi 228
                                        a+l+eAd L++ltd+ gL+d+dpr+++dA l+ e ++ ++el+a+ag+++  +G GGm+tKl aa+lA+r+g  ++
  lcl|FitnessBrowser__Marino:GFF520 163 ANLIEADGLIILTDQLGLFDKDPRKHSDACLVTERRAGDRELDAMAGGGAGVLGRGGMQTKLRAARLAARSGAFTV 238
                                        ************************************************9999************************ PP

                          TIGR01027 229 iasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnF 304
                                        i+ g+ +  i +l ++  +gtl+ +++ ++ +rkqw++ +++++G++++d+ga++ l   g+sLlp+gv +v+g+F
  lcl|FitnessBrowser__Marino:GFF520 239 IVGGRIEGVIGRLRQGDVIGTLLLPEQGRIAARKQWLASHLQTRGRLTLDDGAVKVLCLGGRSLLPVGVKGVSGQF 314
                                        **************************************************************************** PP

                          TIGR01027 305 srgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlvl 363
                                        +rge+v++ +++g+ei++glvny+++e + i+g++s+ i+++Lgy + ee +hrdnlv+
  lcl|FitnessBrowser__Marino:GFF520 315 RRGEMVSCFDQSGREIARGLVNYDADEARAIAGRSSDRITEILGYMSGEEMIHRDNLVI 373
                                        ********************************************************985 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: 8.98
//
[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