Alignments for a candidate for asp-kinase in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Herbaspirillum seropedicae SmR1

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate HSERO_RS10695 HSERO_RS10695 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__HerbieS:HSERO_RS10695
          Length = 417

 Score =  515 bits (1327), Expect = e-151
 Identities = 270/417 (64%), Positives = 330/417 (79%), Gaps = 12/417 (2%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MAL V K+GGTS+GS+ERI+ VA +V K+ DAG  +VVV SAMSGETNRL+ +AK I   
Sbjct: 1   MALYVHKYGGTSMGSIERIQNVAKRVAKWHDAGHQIVVVPSAMSGETNRLLGMAKEIMA- 59

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
            QP  RELD++ STGEQV++ALLA+AL   G  AVSY G QV I TDSA TKARI  IDD
Sbjct: 60  -QPDGRELDMLASTGEQVSVALLAIALQALGKQAVSYAGWQVPIKTDSAFTKARIRSIDD 118

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
            K+R DL AG++V++ GFQGVD  GNITTLGRGGSDT+ VA+AAA+KA EC IYTDVDGV
Sbjct: 119 AKVRKDLNAGKIVIITGFQGVDADGNITTLGRGGSDTSAVAVAAAIKAAECLIYTDVDGV 178

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKE---- 236
           YTTDPRVVS A+RL  +TFEEMLEMASLGSKVLQIR+VEFAG Y +P RVL S  +    
Sbjct: 179 YTTDPRVVSEARRLKTVTFEEMLEMASLGSKVLQIRSVEFAGNYKMPTRVLSSLTDPLTP 238

Query: 237 -----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANI 291
                  GTLI+ +E+++MEQ  I+GIAF+RDEAK+T+ GVPD PG+A++ILGP++ ANI
Sbjct: 239 LAEEAASGTLISFEEDKNMEQATITGIAFSRDEAKITVLGVPDRPGIAYQILGPVADANI 298

Query: 292 EVDMIVQNVSHDNTTDFTFTVHRNEYDAAERILQNTAK-EIGAREVVGDTKIAKVSIVGV 350
           EVDMI+QN S +  TDFTFTV R EY  A  +L N+ K  IGA  + GDTK++KVS+VGV
Sbjct: 299 EVDMIIQNQSVEGKTDFTFTVPRGEYAKAVEVLNNSVKAHIGAAAINGDTKVSKVSVVGV 358

Query: 351 GMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 407
           GMRSH G+AS+MF  L++E +NIQMISTSEIK+SV+I+EKY+ELAVRALH AF+LD+
Sbjct: 359 GMRSHVGIASQMFRTLSEEGVNIQMISTSEIKISVLIDEKYMELAVRALHKAFDLDS 415


Lambda     K      H
   0.316    0.133    0.357 

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: 507
Number of extensions: 18
Number of successful extensions: 4
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: 413
Length of database: 417
Length adjustment: 31
Effective length of query: 382
Effective length of database: 386
Effective search space:   147452
Effective search space used:   147452
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate HSERO_RS10695 HSERO_RS10695 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

# 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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.2884069.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   9.6e-133  429.4   9.0   2.9e-129  417.9   9.0    2.0  1  FitnessBrowser__HerbieS:HSERO_RS10695  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS10695  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.9   9.0  2.9e-129  2.9e-129       1     440 [.       1     411 [.       1     413 [. 0.95

  Alignments for each domain:
  == domain 1  score: 417.9 bits;  conditional E-value: 2.9e-129
                              TIGR00657   1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekeliekirek 72 
                                            mal V K+GGtS+g++eri++vak+v k +  g+q vVV SAm+g T++L+ +a++++ ++           
  FitnessBrowser__HerbieS:HSERO_RS10695   1 MALYVHKYGGTSMGSIERIQNVAKRVAKWHDAGHQIVVVPSAMSGETNRLLGMAKEIMAQP----------- 61 
                                            6788*********************************************************........... PP

                              TIGR00657  73 hlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllgaeagilt 144
                                                                           reld++ s+GE++S+alla al++lg +avs+ g++ +i t
  FitnessBrowser__HerbieS:HSERO_RS10695  62 ---------D--------------------GRELDMLASTGEQVSVALLAIALQALGKQAVSYAGWQVPIKT 104
                                            .........3....................69**************************************** PP

                              TIGR00657 145 dsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDV 216
                                            ds+f++A+ +++i+ +++ k l++g+iv+++GF+G++ +g+ittLGRGGSD++A+++Aaa+kA e+ iytDV
  FitnessBrowser__HerbieS:HSERO_RS10695 105 DSAFTKAR-IRSIDDAKVRKDLNAGKIVIITGFQGVDADGNITTLGRGGSDTSAVAVAAAIKAAECLIYTDV 175
                                            ********.*************************************************************** PP

                              TIGR00657 217 dGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkst........fnpeaeGT 280
                                            dG+yt+DPr+v+eArrl+++++eE+lE+aslG+kvL+ r++e+a ++k p +v s+         ++ a GT
  FitnessBrowser__HerbieS:HSERO_RS10695 176 DGVYTTDPRVVSEARRLKTVTFEEMLEMASLGSKVLQIRSVEFAGNYKMPTRVLSSltdpltplAEEAASGT 247
                                            *****************************************************98732222222356789** PP

                              TIGR00657 281 livaksk.seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsss...etsisfvv 348
                                            li  +++ ++e+  ++++++++++a+++v g++++pgi+ +++g +a+a+++vd+i+q++s   +t  +f+v
  FitnessBrowser__HerbieS:HSERO_RS10695 248 LISFEEDkNMEQATITGIAFSRDEAKITVLGVPDRPGIAYQILGPVADANIEVDMIIQNQSvegKTDFTFTV 319
                                            **8776669999*********************************************9999655555***** PP

                              TIGR00657 349 dkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseiki 420
                                            ++ ++ ka+e+l+++vk++     ++ ++k+++vs+vG gm+s+ g+a+++f +L+ee++ni+mis+seiki
  FitnessBrowser__HerbieS:HSERO_RS10695 320 PRGEYAKAVEVLNNSVKAHIGAAAINGDTKVSKVSVVGVGMRSHVGIASQMFRTLSEEGVNIQMISTSEIKI 391
                                            ************************************************************************ PP

                              TIGR00657 421 svvvdekdaekavealhekl 440
                                            sv++dek++e av+alh+++
  FitnessBrowser__HerbieS:HSERO_RS10695 392 SVLIDEKYMELAVRALHKAF 411
                                            ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (417 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: 14.77
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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