Alignments for a candidate for asp-kinase in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Xanthobacter autotrophicus Py2

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012114646.1 XAUT_RS13210 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_000017645.1:WP_012114646.1
          Length = 419

 Score =  405 bits (1040), Expect = e-117
 Identities = 222/419 (52%), Positives = 294/419 (70%), Gaps = 14/419 (3%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60
           MA +V KFGGTSV +IERI  VA  VK+  EAG  + VV+SAMSG+TN L+   K  +  
Sbjct: 1   MARLVMKFGGTSVANIERIRNVARHVKREVEAGYQVAVVVSAMSGKTNELVGWCKDASAL 60

Query: 61  PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120
             PRE D +V++GEQVT  LL + L + G+ A S+ G Q+ I TD +H  ARIL ID +K
Sbjct: 61  YDPREYDAVVASGEQVTSGLLAIVLQEMGLSARSWQGWQLPISTDDAHGSARILDIDSEK 120

Query: 121 IRADLKEGRVVVVAGFQGVD-EHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179
           + A +  G+V V+AGFQG+    G +TTLGRGGSDT+ VA+AAALKA+ C IYTDVDGVY
Sbjct: 121 LGAAIDGGQVAVIAGFQGIHLPTGRLTTLGRGGSDTSAVAVAAALKAERCDIYTDVDGVY 180

Query: 180 TTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFK------ 233
           TTDPRVVP+ARRL++I FEEMLEMASLG+KVLQ+RSVE A  +NV   V  S        
Sbjct: 181 TTDPRVVPKARRLDRIAFEEMLEMASLGAKVLQVRSVELAMVHNVRTFVRSSLVDPDAPE 240

Query: 234 ----EGPGTLITIDEE---ESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISA 286
               E  GTLI  +EE     ME  +++GIAF++DEA+++IR V D PG+A  + GP++ 
Sbjct: 241 TANVEKAGTLICDEEEIVANQMESQVVTGIAFSKDEAQVSIRRVADKPGIAAAVFGPLAD 300

Query: 287 SNIEVDMIVQNVAHDNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIV 346
           ++I VDMIVQNV+ D  TD TFTV   ++E+A++V+E     I  + V G T + KVS++
Sbjct: 301 AHINVDMIVQNVSADGFTDITFTVPTADFERAKAVIEKARDTIAHQVVEGATDVTKVSVI 360

Query: 347 GVGMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLDA 405
           G+GMRSHAGVA+  F+ALA + INI+ I+TSEIK+S +++  Y ELAVR LH+ + LD+
Sbjct: 361 GIGMRSHAGVAAQAFQALAGKGINIRAITTSEIKISFLIDAAYTELAVRTLHSLYGLDS 419


Lambda     K      H
   0.316    0.133    0.358 

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: 422
Number of extensions: 15
Number of successful extensions: 4
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: 411
Length of database: 419
Length adjustment: 31
Effective length of query: 380
Effective length of database: 388
Effective search space:   147440
Effective search space used:   147440
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_012114646.1 XAUT_RS13210 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm
# target sequence database:        /tmp/gapView.25179.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-125  405.0  10.4   2.2e-125  404.8  10.4    1.0  1  lcl|NCBI__GCF_000017645.1:WP_012114646.1  XAUT_RS13210 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017645.1:WP_012114646.1  XAUT_RS13210 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.8  10.4  2.2e-125  2.2e-125       4     404 ..       4     415 ..       1     418 [. 0.95

  Alignments for each domain:
  == domain 1  score: 404.8 bits;  conditional E-value: 2.2e-125
                                 TIGR00656   4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 
                                                V+KFGGtsv+++eri+++a++v++e++ g++v VVvSAms++t+elv         +  s    pre 
  lcl|NCBI__GCF_000017645.1:WP_012114646.1   4 LVMKFGGTSVANIERIRNVARHVKREVEAGYQVAVVVSAMSGKTNELVGWC------KDASALYDPREY 66 
                                               69*************************************************......8999999***** PP

                                 TIGR00656  73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141
                                               d +v+ GE+++s ll+ +l+e g  a++ +g++ +i Tdd +g+A+i +++  e+L   ++ g++ v+a
  lcl|NCBI__GCF_000017645.1:WP_012114646.1  67 DAVVASGEQVTSGLLAIVLQEMGLSARSWQGWQLPISTDDAHGSARILDIDS-EKLGAAIDGGQVAVIA 134
                                               ****************************************************.**************** PP

                                 TIGR00656 142 GFiGat.eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209
                                               GF+G     G+ TtLGRGGSD++A+++aaalkA+r++iyTDV+GvyttDPrvv++a+++d+i++eE+le
  lcl|NCBI__GCF_000017645.1:WP_012114646.1 135 GFQGIHlPTGRLTTLGRGGSDTSAVAVAAALKAERCDIYTDVDGVYTTDPRVVPKARRLDRIAFEEMLE 203
                                               ****87479************************************************************ PP

                                 TIGR00656 210 lAtlGakvlhpralelaveakvpilvrss.........keke.egTlitn.......kkensslvkaia 261
                                               +A+lGakvl+ r++ela+  +v  +vrss          + e +gTli++       ++e + +v++ia
  lcl|NCBI__GCF_000017645.1:WP_012114646.1 204 MASLGAKVLQVRSVELAMVHNVRTFVRSSlvdpdapetANVEkAGTLICDeeeivanQMESQ-VVTGIA 271
                                               **************************9874333332224555689***99898887555555.****** PP

                                 TIGR00656 262 leknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLke 327
                                               ++k+ a+++++   +++k+gi+a +f+ La+++invd+i+q  s    t+i+++v + d ++ak+++++
  lcl|NCBI__GCF_000017645.1:WP_012114646.1 272 FSKDEAQVSIR--RVADKPGIAAAVFGPLADAHINVDMIVQNVSAdgfTDITFTVPTADFERAKAVIEK 338
                                               ***********..****************************9988899********************* PP

                                 TIGR00656 328 esgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaeka 396
                                                 + +  + +e   d+++vs++g g++++ Gva+++f+al+ k+ini  i++se+kis+l+d +++e a
  lcl|NCBI__GCF_000017645.1:WP_012114646.1 339 ARDTIAHQVVEGATDVTKVSVIGIGMRSHAGVAAQAFQALAGKGINIRAITTSEIKISFLIDAAYTELA 407
                                               *9999999************************************************************* PP

                                 TIGR00656 397 vrklhekl 404
                                               vr+lh+ +
  lcl|NCBI__GCF_000017645.1:WP_012114646.1 408 VRTLHSLY 415
                                               *****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (419 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: 00:00:00.02
# Mc/sec: 7.55
//
[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