GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Echinicola vietnamensis KMM 6221, DSM 17526

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate Echvi_2000 Echvi_2000 aspartate kinase

Query= reanno::Cola:Echvi_2000
         (815 letters)



>FitnessBrowser__Cola:Echvi_2000
          Length = 815

 Score = 1597 bits (4136), Expect = 0.0
 Identities = 815/815 (100%), Positives = 815/815 (100%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES
Sbjct: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV
Sbjct: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD
Sbjct: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180

Query: 181 DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT 240
           DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT
Sbjct: 181 DIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVYT 240

Query: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGEG 300
           AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGEG
Sbjct: 241 AFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGEG 300

Query: 301 KIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVAIA 360
           KIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVAIA
Sbjct: 301 KIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVAIA 360

Query: 361 SKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALGRN 420
           SKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALGRN
Sbjct: 361 SKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALGRN 420

Query: 421 NVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKALTK 480
           NVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKALTK
Sbjct: 421 NVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKALTK 480

Query: 481 MIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGTMT 540
           MIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGTMT
Sbjct: 481 MIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGTMT 540

Query: 541 EMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRGVR 600
           EMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRGVR
Sbjct: 541 EMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRGVR 600

Query: 601 FFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQAKE 660
           FFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQAKE
Sbjct: 601 FFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQAKE 660

Query: 661 KGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFKKL 720
           KGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFKKL
Sbjct: 661 KGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFKKL 720

Query: 721 QKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFTTE 780
           QKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFTTE
Sbjct: 721 QKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFTTE 780

Query: 781 RYNDFPMIVRGPGAGADVTAAGVFADIIRLGNYSR 815
           RYNDFPMIVRGPGAGADVTAAGVFADIIRLGNYSR
Sbjct: 781 RYNDFPMIVRGPGAGADVTAAGVFADIIRLGNYSR 815


Lambda     K      H
   0.317    0.134    0.375 

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: 2059
Number of extensions: 66
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: 815
Length of database: 815
Length adjustment: 41
Effective length of query: 774
Effective length of database: 774
Effective search space:   599076
Effective search space used:   599076
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: 56 (26.2 bits)

Align candidate Echvi_2000 Echvi_2000 (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.6306.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   4.5e-122  394.2   5.6     6e-122  393.8   5.6    1.2  1  lcl|FitnessBrowser__Cola:Echvi_2000  Echvi_2000 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2000  Echvi_2000 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.8   5.6    6e-122    6e-122       5     441 ..       3     457 ..       1     458 [. 0.95

  Alignments for each domain:
  == domain 1  score: 393.8 bits;  conditional E-value: 6e-122
                            TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhlea 76 
                                          + KFGG+S++n e+i+kv  i+++++ek+   + V SA +gvT++L++ a+ +++ ee  ++++++++++hle+
  lcl|FitnessBrowser__Cola:Echvi_2000   3 IIKFGGSSIANYENIQKVFSIIEQKSEKE-AFALVFSAFGGVTEQLLQCANIAQQSEEsyHTILQELEKRHLEI 75 
                                          68***********************9777.99*****************9999988888899************ PP

                            TIGR00657  77 leelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsllga 138
                                          +++l + + + +  ++++ +++e+              +r++d++ls+GE+lS  +laa l+++g    s+++a
  lcl|FitnessBrowser__Cola:Echvi_2000  76 VKKLVPVQQQSTALTFVKVRFNELGDlfhgiylikecsNRTMDYVLSFGERLSNFILAAGLQAKG-IGTSYVDA 148
                                          *****988888889999999999888999************************************.899***** PP

                            TIGR00657 139 eagiltdsefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeve 211
                                          +  + td++fg+Akv  +++++ ++++ +    i v++GFiG+tekge+tt+GR GSD+tA++ Aaal+A++ve
  lcl|FitnessBrowser__Cola:Echvi_2000 149 RDLVKTDDRFGHAKVNFKTTNKLIQDHFKSHdDIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVE 222
                                          **************777777777787777777****************************************** PP

                            TIGR00657 212 iytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivak 285
                                          i+tDV+G++taDPr+v +A  ++++sy+Ea+EL+++Gakv  p+t++pam+ +ipi +k+tf p++ GT i ++
  lcl|FitnessBrowser__Cola:Echvi_2000 223 IWTDVSGVMTADPRLVYTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKD 296
                                          ************************************************************************99 PP

                            TIGR00657 286 skseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkak 357
                                          s   e +++k++s+ +n ++++v+g++    +g+ ++ fg+la++++n++li+q sse+si  ++  +da++ak
  lcl|FitnessBrowser__Cola:Echvi_2000 297 SG--EGKIIKGISSMDNISILNVQGPGLVevVGVSQRFFGTLANNGINIILISQASSEHSICVAIASKDASRAK 368
                                          55..779********************9999******************************************* PP

                            TIGR00657 358 ellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvde 426
                                          ++ +   + + +  ++ e+++  ++a++++vG++m+++pg  +++f+aL ++n+n+ +i+  sse +is v+ +
  lcl|FitnessBrowser__Cola:Echvi_2000 369 SVIEeefRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALGRNNVNVAAIAqgSSELNISAVITQ 442
                                          **996655566777888999****************************************************** PP

                            TIGR00657 427 kdaekavealheklv 441
                                           d +ka++alhe+++
  lcl|FitnessBrowser__Cola:Echvi_2000 443 ADLQKALNALHEAFF 457
                                          *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (815 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: 00:00:00.02
# Mc/sec: 15.14
//
[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