Alignments for a candidate for asp-kinase in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pedobacter sp. GW460-11-11-14-LB5

Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate CA265_RS23475 CA265_RS23475 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= reanno::Pedo557:CA265_RS23475
         (817 letters)



>FitnessBrowser__Pedo557:CA265_RS23475
          Length = 817

 Score = 1590 bits (4118), Expect = 0.0
 Identities = 817/817 (100%), Positives = 817/817 (100%)

Query: 1   MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY 60
           MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY
Sbjct: 1   MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY 60

Query: 61  DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQIL 120
           DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQIL
Sbjct: 61  DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQIL 120

Query: 121 SYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENKD 180
           SYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENKD
Sbjct: 121 SYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENKD 180

Query: 181 KVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKK 240
           KVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKK
Sbjct: 181 KVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKK 240

Query: 241 AFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDVKAS 300
           AFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDVKAS
Sbjct: 241 AFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDVKAS 300

Query: 301 SLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSITFAV 360
           SLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSITFAV
Sbjct: 301 SLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSITFAV 360

Query: 361 KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNALGR 420
           KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNALGR
Sbjct: 361 KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNALGR 420

Query: 421 NGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKRTLNVFCLGTGNIGKTLF 480
           NGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKRTLNVFCLGTGNIGKTLF
Sbjct: 421 NGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKRTLNVFCLGTGNIGKTLF 480

Query: 481 NQLKEQMPFLAANNDLQVKVTGISNTRKMIFSADGLSLENWETELNTNGEPADLAGFVAK 540
           NQLKEQMPFLAANNDLQVKVTGISNTRKMIFSADGLSLENWETELNTNGEPADLAGFVAK
Sbjct: 481 NQLKEQMPFLAANNDLQVKVTGISNTRKMIFSADGLSLENWETELNTNGEPADLAGFVAK 540

Query: 541 MKALNLPNCVFVDNTAAESPIEFYQGIFESSISVVTCNKKGNSADYAQYKSFKDTARKFG 600
           MKALNLPNCVFVDNTAAESPIEFYQGIFESSISVVTCNKKGNSADYAQYKSFKDTARKFG
Sbjct: 541 MKALNLPNCVFVDNTAAESPIEFYQGIFESSISVVTCNKKGNSADYAQYKSFKDTARKFG 600

Query: 601 VDFYYETNVGAGLPIIRTLRELMMSGDKVARIEAILSGTISYIFNNFKGEAGFYETVKEA 660
           VDFYYETNVGAGLPIIRTLRELMMSGDKVARIEAILSGTISYIFNNFKGEAGFYETVKEA
Sbjct: 601 VDFYYETNVGAGLPIIRTLRELMMSGDKVARIEAILSGTISYIFNNFKGEAGFYETVKEA 660

Query: 661 QELGYTEPDPRDDLNGKDFMRKMLILARDAGYPLEASDVKIDNILPEACLNASSVEDFYS 720
           QELGYTEPDPRDDLNGKDFMRKMLILARDAGYPLEASDVKIDNILPEACLNASSVEDFYS
Sbjct: 661 QELGYTEPDPRDDLNGKDFMRKMLILARDAGYPLEASDVKIDNILPEACLNASSVEDFYS 720

Query: 721 ELQANAAYFENLKQTAANDGKVLRYIGKLEDGNVEISLQMVDDSHPFYMLSGSDNIISFT 780
           ELQANAAYFENLKQTAANDGKVLRYIGKLEDGNVEISLQMVDDSHPFYMLSGSDNIISFT
Sbjct: 721 ELQANAAYFENLKQTAANDGKVLRYIGKLEDGNVEISLQMVDDSHPFYMLSGSDNIISFT 780

Query: 781 TDRYKSRPLVVKGPGAGAEVTAAGVFADIINVGTLNK 817
           TDRYKSRPLVVKGPGAGAEVTAAGVFADIINVGTLNK
Sbjct: 781 TDRYKSRPLVVKGPGAGAEVTAAGVFADIINVGTLNK 817


Lambda     K      H
   0.316    0.133    0.369 

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: 2185
Number of extensions: 73
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: 817
Length of database: 817
Length adjustment: 41
Effective length of query: 776
Effective length of database: 776
Effective search space:   602176
Effective search space used:   602176
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: 56 (26.2 bits)

Align candidate CA265_RS23475 CA265_RS23475 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.19569.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   9.7e-126  406.3   1.2   1.2e-125  405.9   1.2    1.1  1  lcl|FitnessBrowser__Pedo557:CA265_RS23475  CA265_RS23475 bifunctional aspar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS23475  CA265_RS23475 bifunctional aspartate kinase/homoserine dehydrogenase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.9   1.2  1.2e-125  1.2e-125       5     441 ..       3     458 ..       1     459 [. 0.93

  Alignments for each domain:
  == domain 1  score: 405.9 bits;  conditional E-value: 1.2e-125
                                  TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekire 71 
                                                V+KFGGtSvg++e+ik + ++v +ek+k+ ++vVV+SAm+gvT+ L e+ae ++++e+  + +++i++
  lcl|FitnessBrowser__Pedo557:CA265_RS23475   3 VLKFGGTSVGSAENIKTLLRLVGEEKQKN-SPVVVLSAMSGVTNLLTEMAEMAERGEDyDTHLKEIEA 69 
                                                89************************777.9**************************98889****** PP

                                  TIGR00657  72 khlealeelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaalee 127
                                                kh++ + +l + a ++ + + l+  ++e++              +++d ils+GE+ S+ +++ + ++
  lcl|FitnessBrowser__Pedo557:CA265_RS23475  70 KHFAVIRSLLPAAAQNPVFTRLKIFFNELEDllqavanlrelsLQTKDQILSYGERCSTFMISHIASK 137
                                                *******9998888887777777777777767778*******9999************9888776655 PP

                                  TIGR00657 128 lgvkavsllgaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGG 193
                                                  + +  ++++   i tds+fg+Akv +e ++  ++++ +e+  ++  v+GFi+++  g++ttLGRGG
  lcl|FitnessBrowser__Pedo557:CA265_RS23475 138 N-IGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENkdKVLFVTGFIASNAAGRVTTLGRGG 204
                                                4.467778888999***********88888888889999988899*********************** PP

                                  TIGR00657 194 SDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepam 261
                                                SD+tAa+ +aal+A+e+ei+tDV+G +taDPr+v++A  l+e+sy Ea+EL+++Gakv++p t+ pa 
  lcl|FitnessBrowser__Pedo557:CA265_RS23475 205 SDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAF 272
                                                ******************************************************************** PP

                                  TIGR00657 262 rakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalae 327
                                                 +kipiv+k+tf+p+  GT i ++ k ++  ++k++s+ ++ +++++ g++m   +g+  ++f+ l++
  lcl|FitnessBrowser__Pedo557:CA265_RS23475 273 MKKIPIVIKNTFEPDFAGTYIKSDVKASS-LPIKGISSIDHISIINLTGSGMVgkAGFSGRLFSLLSR 339
                                                ************************99666.**********************999************* PP

                                  TIGR00657 328 akvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksa 392
                                                +++nv+li+qssse+si+f+v+ +da++a +l k   + ++++k+le  eve++la+ ++vG++mk +
  lcl|FitnessBrowser__Pedo557:CA265_RS23475 340 EQINVVLITQSSSEHSITFAVKPTDASQAISLIKkefELELDAKKLELPEVENNLAVLAIVGENMKRT 407
                                                ********************************9966655667777777789***************** PP

                                  TIGR00657 393 pgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                                pg+ +++f+aL +++in+++i+  sse++isv+++++d  kav+a+h++++
  lcl|FitnessBrowser__Pedo557:CA265_RS23475 408 PGMSGRLFNALGRNGINVRAIAqgSSEYNISVIISKDDLSKAVNAVHDAFF 458
                                                *************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (817 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: 11.28
//
[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