Alignments for a candidate for proB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Sinorhizobium meliloti 1021

Align Glutamate 5-kinase 2; EC 2.7.2.11; Gamma-glutamyl kinase 2; GK 2 (uncharacterized)
to candidate SMc03252 SMc03252 gamma-glutamyl kinase

Query= curated2:Q92LF7
         (269 letters)



>FitnessBrowser__Smeli:SMc03252
          Length = 282

 Score =  518 bits (1335), Expect = e-152
 Identities = 269/269 (100%), Positives = 269/269 (100%)

Query: 1   MEDKFDLSSARLVVVKIGSTLVLDRETSGIRSSWLESLTEDVSRLLTRGQQVVLVSSGAV 60
           MEDKFDLSSARLVVVKIGSTLVLDRETSGIRSSWLESLTEDVSRLLTRGQQVVLVSSGAV
Sbjct: 14  MEDKFDLSSARLVVVKIGSTLVLDRETSGIRSSWLESLTEDVSRLLTRGQQVVLVSSGAV 73

Query: 61  AIGSTIVDRLATYSQVSHKQAAAALGQVQLTHAYSESLKRHGLQVAQLLMGRGDLVDPAH 120
           AIGSTIVDRLATYSQVSHKQAAAALGQVQLTHAYSESLKRHGLQVAQLLMGRGDLVDPAH
Sbjct: 74  AIGSTIVDRLATYSQVSHKQAAAALGQVQLTHAYSESLKRHGLQVAQLLMGRGDLVDPAH 133

Query: 121 RLNTRAVLLRLIDLGAVPLVNENDTTATCGTRVGDNDRLAAWIAEIINADLLILLSNVDG 180
           RLNTRAVLLRLIDLGAVPLVNENDTTATCGTRVGDNDRLAAWIAEIINADLLILLSNVDG
Sbjct: 134 RLNTRAVLLRLIDLGAVPLVNENDTTATCGTRVGDNDRLAAWIAEIINADLLILLSNVDG 193

Query: 181 LFMKDPRNNPLTPMLTEVESITREIEAMATQSVDPYSSGGMISKIEAGKIAMNAGCRMII 240
           LFMKDPRNNPLTPMLTEVESITREIEAMATQSVDPYSSGGMISKIEAGKIAMNAGCRMII
Sbjct: 194 LFMKDPRNNPLTPMLTEVESITREIEAMATQSVDPYSSGGMISKIEAGKIAMNAGCRMII 253

Query: 241 ANGTRSHPLYAIESGGPSTHFIPVARDRV 269
           ANGTRSHPLYAIESGGPSTHFIPVARDRV
Sbjct: 254 ANGTRSHPLYAIESGGPSTHFIPVARDRV 282


Lambda     K      H
   0.318    0.132    0.368 

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: 416
Number of extensions: 3
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: 269
Length of database: 282
Length adjustment: 25
Effective length of query: 244
Effective length of database: 257
Effective search space:    62708
Effective search space used:    62708
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: 47 (22.7 bits)

Align candidate SMc03252 SMc03252 (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.4037.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      4e-73  232.6   0.3    4.7e-73  232.3   0.3    1.0  1  lcl|FitnessBrowser__Smeli:SMc03252  SMc03252 gamma-glutamyl kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03252  SMc03252 gamma-glutamyl kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.3   0.3   4.7e-73   4.7e-73       3     242 ..      26     266 ..      24     281 .. 0.95

  Alignments for each domain:
  == domain 1  score: 232.3 bits;  conditional E-value: 4.7e-73
                           TIGR01027   3 iVvKlGsssLteesgk.lkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQ 76 
                                         +VvK+Gs+++ + +++ +++s l++l+e+v++l + G++vv+vsSGava G +  +      ++++kQa+aa GQ
  lcl|FitnessBrowser__Smeli:SMc03252  26 VVVKIGSTLVLDRETSgIRSSWLESLTEDVSRLLTRGQQVVLVSSGAVAIGSTIVDRLATYSQVSHKQAAAALGQ 100
                                         8*******999888888********************************************************** PP

                           TIGR01027  77 grLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsal 151
                                         ++L ++y+++++++gl+vaQ+L+ r dl +  + lN r+ l +l++lg+vp+vNENDt+a+   ++GDND+L+a 
  lcl|FitnessBrowser__Smeli:SMc03252 101 VQLTHAYSESLKRHGLQVAQLLMGRGDLVDPAHRLNTRAVLLRLIDLGAVPLVNENDTTATCGTRVGDNDRLAAW 175
                                         *************************************************************************** PP

                           TIGR01027 152 vaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragve 226
                                         +a +++AdlL+ll++vdgL+ +dpr+np   ++ eve+i++e++a+a++s   +  GGm +K+ea ++A++ag +
  lcl|FitnessBrowser__Smeli:SMc03252 176 IAEIINADLLILLSNVDGLFMKDPRNNPLTPMLTEVESITREIEAMATQSVDPYSSGGMISKIEAGKIAMNAGCR 250
                                         *************************************************************************** PP

                           TIGR01027 227 viiasgekpekiadll 242
                                         +iia+g++ + + ++ 
  lcl|FitnessBrowser__Smeli:SMc03252 251 MIIANGTRSHPLYAIE 266
                                         *******977766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (282 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: 8.35
//
[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