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

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.32675.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.04
//
[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