Alignments for a candidate for proB in Azospirillum brasilense Sp245

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.12327.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.69
//
[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