Alignments for a candidate for asp-kinase in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Shewanella oneidensis MR-1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 202534 SO3427 aspartokinase (NCBI ptt file)

Query= BRENDA::O69077
         (412 letters)



>FitnessBrowser__MR1:202534
          Length = 418

 Score =  348 bits (893), Expect = e-100
 Identities = 197/408 (48%), Positives = 278/408 (68%), Gaps = 8/408 (1%)

Query: 3   LIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQPV 62
           L V+KFGGTSVG++ERIE VAE++ K   +G+  V+V+SAM+GETNRL  LA QI  +  
Sbjct: 12  LFVKKFGGTSVGSIERIEVVAEQIAKSAHSGEQQVLVLSAMAGETNRLFALAAQIDPRAS 71

Query: 63  PRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTHIR 122
            RELD++VSTGEQ++IAL++MAL +RG+ A S TG+QV+I T+S   +A I  +D  ++ 
Sbjct: 72  ARELDMLVSTGEQISIALMAMALQRRGIKARSLTGDQVQIHTNSQFGRASIESVDTAYLT 131

Query: 123 ADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
           + L+ G V +VAGFQG+D NG++TTLGRGGSDTT VALAAAL+ADECQI+TDV GV+TTD
Sbjct: 132 SLLEQGIVPIVAGFQGIDPNGDVTTLGRGGSDTTAVALAAALRADECQIFTDVSGVFTTD 191

Query: 183 PRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLITI 242
           P +   ARRLD I F+ MLEMA LG+KVL   +VE+A ++ VPLRVL SF+ G GTLI  
Sbjct: 192 PNIDSSARRLDVIGFDVMLEMAKLGAKVLHPDSVEYAQRFKVPLRVLSSFEAGQGTLIQF 251

Query: 243 DDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMI----VQN 298
            DE E      + GIA N+  A LTI G+  +      +L  ++   V+V+ I    +  
Sbjct: 252 GDESELAMAASVQGIAINKALATLTIEGLFTSSERYQALLACLARLEVDVEFITPLKLNE 311

Query: 299 VAHDNTTDFTFTVHRND-YLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGV 357
           ++   +  F     + D  L+ LE+L +   ++   + I +   AKVS+VG G+++  G+
Sbjct: 312 ISPVESVSFMLAEAKVDILLHELEVLSE---SLDLGQLIVERQRAKVSLVGKGLQAKVGL 368

Query: 358 ASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405
            ++M + L  E+I+ +++STSE K+S VI+E+ L  AVRALH AFEL+
Sbjct: 369 LTKMLDVLGNETIHAKLLSTSESKLSTVIDERDLHKAVRALHHAFELN 416


Lambda     K      H
   0.317    0.133    0.362 

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: 425
Number of extensions: 13
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: 412
Length of database: 418
Length adjustment: 31
Effective length of query: 381
Effective length of database: 387
Effective search space:   147447
Effective search space used:   147447
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: 50 (23.9 bits)

Align candidate 202534 SO3427 (aspartokinase (NCBI ptt file))
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.1344168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
   4.6e-122  394.2   6.0   6.3e-106  341.0   1.7    2.0  2  FitnessBrowser__MR1:202534  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__MR1:202534  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.1   1.7e-19   1.7e-19       2      61 ..      11      70 ..      10      73 .. 0.95
   2 !  341.0   1.7  6.3e-106  6.3e-106     103     441 ..      72     414 ..      69     415 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.7e-19
                   TIGR00657  2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvssee 61
                                +l V KFGGtSvg++eri+ va+ + k++++g+q v V+SAmag T++L +la ++++++
  FitnessBrowser__MR1:202534 11 KLFVKKFGGTSVGSIERIEVVAEQIAKSAHSGEQQVLVLSAMAGETNRLFALAAQIDPRA 70
                                6789***************************************************99876 PP

  == domain 2  score: 341.0 bits;  conditional E-value: 6.3e-106
                   TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekge 185
                                  reld+++s+GE++S+al+a+al+++g+ka+sl+g++ +i t+s+fgrA+ +e+++t+ l++lle+gi+++vaGF+G++++g+
  FitnessBrowser__MR1:202534  72 ARELDMLVSTGEQISIALMAMALQRRGIKARSLTGDQVQIHTNSQFGRAS-IESVDTAYLTSLLEQGIVPIVAGFQGIDPNGD 153
                                 689***********************************************.******************************** PP

                   TIGR00657 186 ittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipiv 268
                                 +ttLGRGGSD+tA++lAaal+Ade++i+tDV+G++t+DP+i ++Arrld i ++ +lE+a+lGakvLhp+++e+a r+k+p++
  FitnessBrowser__MR1:202534 154 VTTLGRGGSDTTAVALAAALRADECQIFTDVSGVFTTDPNIDSSARRLDVIGFDVMLEMAKLGAKVLHPDSVEYAQRFKVPLR 236
                                 *********************************************************************************** PP

                   TIGR00657 269 vkstfnpeaeGTlivaksk..seeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlil....qsssets.. 343
                                 v s+f+   +GTli   ++     +  v++++ +k  a ++++g    ++  + ++ +la+ +v+v+ i+        e s  
  FitnessBrowser__MR1:202534 237 VLSSFEAG-QGTLIQFGDEseLAMAASVQGIAINKALATLTIEGLFTSSERYQALLACLARLEVDVEFITplklN---EISpv 315
                                 ******99.*****9888877444589*******************************************95542...33333 PP

                   TIGR00657 344 ..isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvv 424
                                   +sf++ + ++d   ++l + + e  +l+++ ve++ a+vslvG+g++ + g+++k++++L +e i  + +s+se k+s+v+
  FitnessBrowser__MR1:202534 316 esVSFMLAEAKVDILLHEL-EVLSESLDLGQLIVERQRAKVSLVGKGLQAKVGLLTKMLDVLGNETIHAKLLSTSESKLSTVI 397
                                 45**************998.68999999******************************************************* PP

                   TIGR00657 425 dekdaekavealheklv 441
                                 de+d +kav+alh++++
  FitnessBrowser__MR1:202534 398 DERDLHKAVRALHHAFE 414
                                 **************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (418 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: 9.46
//
[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