GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Azospirillum brasilense Sp245

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate AZOBR_RS04095 AZOBR_RS04095 glutamate 5-kinase

Query= reanno::Korea:Ga0059261_3512
         (367 letters)



>FitnessBrowser__azobra:AZOBR_RS04095
          Length = 376

 Score =  332 bits (850), Expect = 1e-95
 Identities = 196/369 (53%), Positives = 247/369 (66%), Gaps = 16/369 (4%)

Query: 11  RLVVKIGSALLVDPE-GAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGARRLKLAK 69
           RLVVKIGSALLVD   G +RR+WL+ +A D+AA  + GQ++ +V+SGA+A G   L L  
Sbjct: 10  RLVVKIGSALLVDSATGRMRREWLDALADDVAACRKRGQEVVIVTSGAVACGREHLGLV- 68

Query: 70  GGRA-SLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNAAATLG 128
            GRA  LE+ QAAAATGQI L+  + E LA +GLT AQ+LVTL+D E+RRR+LN  AT+ 
Sbjct: 69  -GRALRLEEKQAAAATGQIRLAAAYQETLARHGLTVAQVLVTLEDTEERRRHLNGRATID 127

Query: 129 RLLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDRNPAL- 187
            LL LG VPVINEND+VATAEIRFGDNDRLAARVAQ   A  +VLLSDIDGLY  +P   
Sbjct: 128 TLLKLGAVPVINENDTVATAEIRFGDNDRLAARVAQMISADTLVLLSDIDGLYTADPRKD 187

Query: 188 PGAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIANGRVDRP 247
           P A HIPVV+ +   +E MA      G  SGGMV+KI AAR+A +AG  + IA G+   P
Sbjct: 188 PDARHIPVVQELTSDIENMAGE-PPPGYSSGGMVTKIVAARVALAAGCRMVIAKGKRMNP 246

Query: 248 LSA--------DARHTVFLP-EKRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLA 298
           L+A         A  T FLP    + ARKAW+ G L A G++ VDAGA  AL  G SLL 
Sbjct: 247 LAALEQRPEQGGALCTWFLPAASPSSARKAWIGGNLNAHGALTVDAGALSALARGASLLP 306

Query: 299 IGATAIRGMFFRGDLVTIEGPNG-PIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRST 357
            G  A+ G F RGD+V ++ P+G  +ARGL+ Y A DA+ I G +S +  EILGY  R  
Sbjct: 307 AGVRAVEGDFERGDVVVVKAPDGREVARGLTAYAAEDARRIAGRKSHEIEEILGYRGRDE 366

Query: 358 LVHRNHMAL 366
           ++HR+ + +
Sbjct: 367 MIHRDDLVV 375


Lambda     K      H
   0.319    0.134    0.377 

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: 412
Number of extensions: 22
Number of successful extensions: 6
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: 376
Length adjustment: 30
Effective length of query: 337
Effective length of database: 346
Effective search space:   116602
Effective search space used:   116602
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate AZOBR_RS04095 AZOBR_RS04095 (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.12548.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-126  406.5   0.0   6.1e-126  406.4   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS04095  AZOBR_RS04095 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS04095  AZOBR_RS04095 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.4   0.0  6.1e-126  6.1e-126       1     362 [.       9     374 ..       9     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 406.4 bits;  conditional E-value: 6.1e-126
                                 TIGR01027   1 kriVvKlGsssLteesgk.lkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaek 68 
                                               +r+VvK+Gs++L+++ +  ++r+ l +l+ +va+ +k G+evviv+SGava G e+Lgl  r  +l+ek
  lcl|FitnessBrowser__azobra:AZOBR_RS04095   9 RRLVVKIGSALLVDSATGrMRREWLDALADDVAACRKRGQEVVIVTSGAVACGREHLGLVGRALRLEEK 77 
                                               589***********99887************************************************** PP

                                 TIGR01027  69 QalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvav 137
                                               Qa+aa GQ rL ++y+++++++gl+vaQ+L t +d ++r+r+lN r+t+++ll+lg+vp++NENDtva+
  lcl|FitnessBrowser__azobra:AZOBR_RS04095  78 QAAAATGQIRLAAAYQETLARHGLTVAQVLVTLEDTEERRRHLNGRATIDTLLKLGAVPVINENDTVAT 146
                                               ********************************************************************* PP

                                 TIGR01027 138 eeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvG 206
                                               +ei+fGDND+L+a va++++Ad+Lvll+d+dgLy+adpr++pdA+ i++v+e++++++++ag+ +  + 
  lcl|FitnessBrowser__azobra:AZOBR_RS04095 147 AEIRFGDNDRLAARVAQMISADTLVLLSDIDGLYTADPRKDPDARHIPVVQELTSDIENMAGEPPPGYS 215
                                               ****************************************************************999** PP

                                 TIGR01027 207 TGGmrtKleaaelAsragveviiasgekpekiadlle....daavgtlfeakkkklknrkqwilaasea 271
                                                GGm tK+ aa++A +ag +++ia+g++ + +a+l +    + a+ t f + ++  ++rk+wi  +++a
  lcl|FitnessBrowser__azobra:AZOBR_RS04095 216 SGGMVTKIVAARVALAAGCRMVIAKGKRMNPLAALEQrpeqGGALCTWFLPAASPSSARKAWIGGNLNA 284
                                               *****************************999998874444566779********************** PP

                                 TIGR01027 272 kGkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglks 340
                                               +G+++vd+ga +al + g+sLlpagv +veg+F+rg+vv ++a++g+e+++gl++y +e+ ++i+g+ks
  lcl|FitnessBrowser__azobra:AZOBR_RS04095 285 HGALTVDAGALSALAR-GASLLPAGVRAVEGDFERGDVVVVKAPDGREVARGLTAYAAEDARRIAGRKS 352
                                               **************98.**************************************************** PP

                                 TIGR01027 341 eeiedvLgyekkeevvhrdnlv 362
                                               +eie++Lgy+ ++e +hrd+lv
  lcl|FitnessBrowser__azobra:AZOBR_RS04095 353 HEIEEILGYRGRDEMIHRDDLV 374
                                               ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (376 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: 11.80
//
[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:

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:

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:

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:

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