Alignments for a candidate for asp-kinase in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Escherichia coli BW25113

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 14147 b0002 bifunctional aspartokinase I/homeserine dehydrogenase I (NCBI)

Query= BRENDA::P00561
         (820 letters)



>FitnessBrowser__Keio:14147
          Length = 820

 Score = 1599 bits (4141), Expect = 0.0
 Identities = 820/820 (100%), Positives = 820/820 (100%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
Sbjct: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60

Query: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
           LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
Sbjct: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120

Query: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
           ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
Sbjct: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180

Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
           ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
Sbjct: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240

Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
           PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
Sbjct: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300

Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
           EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
Sbjct: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360

Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
           CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
Sbjct: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420

Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480
           ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL
Sbjct: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480

Query: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
           LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
Sbjct: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540

Query: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
           VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
Sbjct: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600

Query: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
           RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
Sbjct: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660

Query: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
           REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
Sbjct: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720

Query: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
           NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
Sbjct: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780

Query: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
           YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
Sbjct: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820


Lambda     K      H
   0.319    0.135    0.384 

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: 1986
Number of extensions: 52
Number of successful extensions: 3
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: 820
Length of database: 820
Length adjustment: 42
Effective length of query: 778
Effective length of database: 778
Effective search space:   605284
Effective search space used:   605284
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: 56 (26.2 bits)

Align candidate 14147 b0002 (bifunctional aspartokinase I/homeserine dehydrogenase I (NCBI))
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.23613.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.9e-157  509.8   0.1   4.8e-157  509.5   0.1    1.1  1  lcl|FitnessBrowser__Keio:14147  b0002 bifunctional aspartokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14147  b0002 bifunctional aspartokinase I/homeserine dehydrogenase I (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.5   0.1  4.8e-157  4.8e-157       5     441 ..       3     460 ..       1     461 [. 0.98

  Alignments for each domain:
  == domain 1  score: 509.5 bits;  conditional E-value: 4.8e-157
                       TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekirekhlealee 79 
                                     V+KFGGtSv+n+er+ +va+i+++++++g qv++V+SA+a++T++Lv+++ek+ s+++     + +e+i+++ l++l++
  lcl|FitnessBrowser__Keio:14147   3 VLKFGGTSVANAERFLRVADILESNARQG-QVATVLSAPAKITNHLVAMIEKTISGQDalpnISDAERIFAELLTGLAA 80 
                                     99************************999.***************************9999999*************** PP

                       TIGR00657  80 lasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltds 146
                                     +++ +  ++lk+++++e++++k+            ++ +++++++GEk+S+a++a++le++g ++v+++++++++l+ +
  lcl|FitnessBrowser__Keio:14147  81 AQPGFPLAQLKTFVDQEFAQIKHvlhgisllgqcpDSINAALICRGEKMSIAIMAGVLEARG-HNVTVIDPVEKLLAVG 158
                                     **************************************************************.**************** PP

                       TIGR00657 147 efgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDP 224
                                     ++++++v + ++t+r+++      ++v++aGF++ +ekge+++LGR+GSD++Aa+lAa+l+Ad++ei+tDVdG+yt+DP
  lcl|FitnessBrowser__Keio:14147 159 HYLESTVDIAESTRRIAASRIPAdHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDP 237
                                     ******999999999988877777******************************************************* PP

                       TIGR00657 225 rivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknq 303
                                     r+vp+Ar+l+++sy+Ea+EL+++GakvLhprt++p+++++ip+++k+t+np+a+GTli+a+++++ e +vk++s+ +n+
  lcl|FitnessBrowser__Keio:14147 238 RQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDED-ELPVKGISNLNNM 315
                                     *************************************************************9955.5************ PP

                       TIGR00657 304 alvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevek 377
                                     a++svsg++mk  +g++a+vf a+++a+++v+li+qssse+sisf+v+++d+ +a+++++     +++e  le++ v++
  lcl|FitnessBrowser__Keio:14147 316 AMFSVSGPGMKgmVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQeefYLELKEGLLEPLAVTE 394
                                     **********************************************************99777668999********** PP

                       TIGR00657 378 klalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                     +la++s+vG+gm++  g+ ak+f+aLa++nini++i+  sse++isvvv+++da++ v+++h++l+
  lcl|FitnessBrowser__Keio:14147 395 RLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAqgSSERSISVVVNNDDATTGVRVTHQMLF 460
                                     ****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (820 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 11.99
//
[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