Alignments for a candidate for asp-kinase in Hyphomicrobium sulfonivorans WDL6

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Hyphomicrobium sulfonivorans WDL6

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_068462230.1 APY04_RS10130 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>NCBI__GCF_001541235.1:WP_068462230.1
          Length = 420

 Score =  393 bits (1009), Expect = e-114
 Identities = 219/420 (52%), Positives = 287/420 (68%), Gaps = 16/420 (3%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           MA++V KFGGTSV  VERI  VA  VK+  D G+ + VVVSAMSG TN+L+   ++ S  
Sbjct: 1   MAVVVMKFGGTSVANVERIRNVARHVKREVDAGNKVCVVVSAMSGVTNQLVAYVREASLL 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
              RE D +V+TGEQVT  LLA+ L   G+ A S+ G QV I   +AH  ARI  ID   
Sbjct: 61  HDAREYDAVVATGEQVTAGLLAIVLQSMGLQARSWQGWQVPITASAAHGSARITGIDGSE 120

Query: 121 IQRDIKAGRVVVVAGFQGVD-EKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179
           I R  ++  V VV GFQG++ E+  + TLGRGGSDT+ VA+A ALKAD C IYTDVDGVY
Sbjct: 121 ILRRFESDEVAVVTGFQGIEPERQRVATLGRGGSDTSAVAMAVALKADVCDIYTDVDGVY 180

Query: 180 TTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSF------- 232
           TTDPR+VAKA+RL KI++EEMLEMASLGSKVLQ R+VE A  + + +RVL SF       
Sbjct: 181 TTDPRIVAKAKRLPKISYEEMLEMASLGSKVLQTRSVELAMNHRMRVRVLSSFVAPEAMA 240

Query: 233 ------QEGPGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISA 286
                  E  GT++  DE+E +E  ++SGIA+ +DEAK+T+  V D PG+A +I GP++ 
Sbjct: 241 PVRLGQLEDIGTVV-CDEDEIVESQVVSGIAYVKDEAKVTLIKVEDKPGIAARIFGPLAD 299

Query: 287 ANVEVDMIVQNVAHDNT-TDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSI 345
           AN+ VDMIVQ+V  D   TD TFTV   +    L+ L+   +E+G  E     ++AK+S+
Sbjct: 300 ANINVDMIVQSVTPDGKHTDMTFTVQATELPRTLETLKAAKSEIGEFEIQSSADVAKISV 359

Query: 346 VGVGMRSHAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 405
           +G+GMRSHAGVA+ MF+AL+ + INI  I+TSEIK+SV+I+  Y ELAVR LH+ + LDA
Sbjct: 360 IGIGMRSHAGVAALMFKALSDKGINILAITTSEIKISVLIDAAYAELAVRTLHSIYGLDA 419


Lambda     K      H
   0.317    0.133    0.357 

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: 397
Number of extensions: 10
Number of successful extensions: 5
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: 420
Length adjustment: 31
Effective length of query: 381
Effective length of database: 389
Effective search space:   148209
Effective search space used:   148209
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: 50 (23.9 bits)

Align candidate WP_068462230.1 APY04_RS10130 (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.24811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-124  402.7  18.3   1.8e-105  339.5   6.7    2.2  2  lcl|NCBI__GCF_001541235.1:WP_068462230.1  APY04_RS10130 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001541235.1:WP_068462230.1  APY04_RS10130 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   3.4   7.2e-24   7.2e-24       1      58 [.       1      58 [.       1      63 [. 0.95
   2 !  339.5   6.7  1.8e-105  1.8e-105      99     440 ..      59     415 ..      55     417 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 7.2e-24
                                 TIGR00657  1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvs 58
                                              ma++V+KFGGtSv+nveri++va++vk+e   gn+v VVvSAm+gvT++Lv+ ++++s
  lcl|NCBI__GCF_001541235.1:WP_068462230.1  1 MAVVVMKFGGTSVANVERIRNVARHVKREVDAGNKVCVVVSAMSGVTNQLVAYVREAS 58
                                              789**************************************************99986 PP

  == domain 2  score: 339.5 bits;  conditional E-value: 1.8e-105
                                 TIGR00657  99 evkkereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklle 167
                                               +++  re+d+++++GE+++a lla +l++ g +a+s+ g++ +i +++++g+A+ ++ i+ ++++   e
  lcl|NCBI__GCF_001541235.1:WP_068462230.1  59 LLHDAREYDAVVATGEQVTAGLLAIVLQSMGLQARSWQGWQVPITASAAHGSAR-ITGIDGSEILRRFE 126
                                               556689************************************************.************** PP

                                 TIGR00657 168 egiivvvaGFiGat.ekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrlde 235
                                                + + vv+GF+G++ e +++ tLGRGGSD++A+++A alkAd+++iytDVdG+yt+DPriv +A+rl++
  lcl|NCBI__GCF_001541235.1:WP_068462230.1 127 SDEVAVVTGFQGIEpERQRVATLGRGGSDTSAVAMAVALKADVCDIYTDVDGVYTTDPRIVAKAKRLPK 195
                                               **************88899************************************************** PP

                                 TIGR00657 236 isyeEalELaslGakvLhprtlepamrakipivvkstf............npeaeGTlivakskseeep 292
                                               isyeE+lE+aslG+kvL+ r++e+am++  +++v s+f            + e  GT+++ +++  e++
  lcl|NCBI__GCF_001541235.1:WP_068462230.1 196 ISYEEMLEMASLGSKVLQTRSVELAMNHRMRVRVLSSFvapeamapvrlgQLEDIGTVVCDEDEIVESQ 264
                                               ***********************************99843322222222233556*********88889 PP

                                 TIGR00657 293 avkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsss....ets.isfvvdkedadka 356
                                                v+++++ k++a+v++ ++++kpgi+a++fg la+a++nvd+i+qs+     + + ++f+v+ ++++++
  lcl|NCBI__GCF_001541235.1:WP_068462230.1 265 VVSGIAYVKDEAKVTLIKVEDKPGIAARIFGPLADANINVDMIVQSVTpdgkH-TdMTFTVQATELPRT 332
                                               ***********************************************976644.26************* PP

                                 TIGR00657 357 kellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvd 425
                                                e l k++k+e    e++   ++a++s++G gm+s+ gvaa +f+aL++++ini +i +seikisv++d
  lcl|NCBI__GCF_001541235.1:WP_068462230.1 333 LETL-KAAKSEIGEFEIQSSADVAKISVIGIGMRSHAGVAALMFKALSDKGINILAITTSEIKISVLID 400
                                               ***8.568888888889999************************************************* PP

                                 TIGR00657 426 ekdaekavealhekl 440
                                                 +ae av++lh+ +
  lcl|NCBI__GCF_001541235.1:WP_068462230.1 401 AAYAELAVRTLHSIY 415
                                               ************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (420 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.18
//
[ok]

This GapMind analysis is from Apr 10 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