Alignments for a candidate for asp-kinase in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Rhodomicrobium vannielii ATCC 17100

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013420319.1 RVAN_RS13760 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_000166055.1:WP_013420319.1
          Length = 418

 Score =  392 bits (1006), Expect = e-113
 Identities = 220/417 (52%), Positives = 285/417 (68%), Gaps = 16/417 (3%)

Query: 3   LIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQPV 62
           L+V KFGGTSV  + RI   A  VK+  EAG+ V VVVSAM+G TN+L+G   +  E   
Sbjct: 2   LLVMKFGGTSVADIARIRNSALHVKREVEAGNRVAVVVSAMAGHTNQLVGWCKEAHELYD 61

Query: 63  PRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTHIR 122
            RE D +VS+GEQVT  L+++ L   GV A S+ G Q+ ++TD +H+ ARI  ++   + 
Sbjct: 62  LREYDAVVSSGEQVTAGLMAIILQSIGVKARSWQGWQIPLVTDGSHSVARIDRLETADLL 121

Query: 123 ADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
           A ++ G V VVAGFQG+  +G ITTLGRGGSDT+ VALAAALKA+ C IYTDVDGVYTTD
Sbjct: 122 ASVEGGEVAVVAGFQGIAPSGRITTLGRGGSDTSAVALAAALKAERCDIYTDVDGVYTTD 181

Query: 183 PRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSF---------- 232
           PR+VP ARRL +I++EEMLEMASLG+KVLQ R+VE A    V ++V  SF          
Sbjct: 182 PRLVPDARRLPRISYEEMLEMASLGAKVLQTRSVELAMAQGVRVQVRSSFDNPESCEPAR 241

Query: 233 ---QEGPGTLITIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAAN 289
               E  GTL+   DE E +E  ++SGIA+ +DEAK+T+  + D PGVA  I  P+S AN
Sbjct: 242 SGISEMCGTLVC--DETEMLEHHVVSGIAYAKDEAKVTVLSIEDKPGVAASIFVPLSEAN 299

Query: 290 VEVDMIVQNVAHD-NTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVG 348
           + VDMIVQN++ D   TD TFTV   +   AL++L+     I  R+  GDT++ KVS++G
Sbjct: 300 INVDMIVQNISEDGRKTDLTFTVAAAELPRALQVLRDNQDTIRYRDLRGDTDMVKVSVIG 359

Query: 349 VGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405
           VGMRSHAGVA+ MF+ALA +SINIQ ISTSEIK+SV+I   + E AV  LH+ F LD
Sbjct: 360 VGMRSHAGVAAEMFQALAGKSINIQAISTSEIKISVLIGAAHTEEAVNTLHSLFGLD 416


Lambda     K      H
   0.317    0.133    0.362 

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: 423
Number of extensions: 19
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: 412
Length of database: 418
Length adjustment: 31
Effective length of query: 381
Effective length of database: 387
Effective search space:   147447
Effective search space used:   147447
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: 50 (23.9 bits)

Align candidate WP_013420319.1 RVAN_RS13760 (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.6425.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-129  418.8   9.1   2.1e-129  418.0   9.1    1.3  1  lcl|NCBI__GCF_000166055.1:WP_013420319.1  RVAN_RS13760 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013420319.1  RVAN_RS13760 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.0   9.1  2.1e-129  2.1e-129       2     405 ..       1     414 [.       1     416 [. 0.95

  Alignments for each domain:
  == domain 1  score: 418.0 bits;  conditional E-value: 2.1e-129
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                               +l V+KFGGtsv+++ ri+++a +v++e++ g++v VVvSAm++ t++lv         +  ++    r
  lcl|NCBI__GCF_000166055.1:WP_013420319.1   1 MLLVMKFGGTSVADIARIRNSALHVKREVEAGNRVAVVVSAMAGHTNQLVGWC------KEAHELYDLR 63 
                                               689**************************************************......8999999*** PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                               e d +vs GE++++ l++ +l+  gvka++ +g++ +++Td+++  A+i++l+t   Ll   e g + v
  lcl|NCBI__GCF_000166055.1:WP_013420319.1  64 EYDAVVSSGEQVTAGLMAIILQSIGVKARSWQGWQIPLVTDGSHSVARIDRLET-ADLLASVEGGEVAV 131
                                               ******************************************************.99************ PP

                                 TIGR00656 140 vaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEal 208
                                               vaGF+G    G+iTtLGRGGSD++A++laaalkA+r++iyTDV+GvyttDPr+v++a+++++isyeE+l
  lcl|NCBI__GCF_000166055.1:WP_013420319.1 132 VAGFQGIAPSGRITTLGRGGSDTSAVALAAALKAERCDIYTDVDGVYTTDPRLVPDARRLPRISYEEML 200
                                               ********************************************************************* PP

                                 TIGR00656 209 elAtlGakvlhpralelaveakvpilvrsskekee.............gTlitnkkens..slvkaial 262
                                               e+A+lGakvl+ r++ela++++v + vrss+++ e             gTl+++++e+   ++v++ia+
  lcl|NCBI__GCF_000166055.1:WP_013420319.1 201 EMASLGAKVLQTRSVELAMAQGVRVQVRSSFDNPEsceparsgisemcGTLVCDETEMLehHVVSGIAY 269
                                               ******************************99744122333333334478888866665559******* PP

                                 TIGR00656 263 eknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLke 327
                                                k+ a++tv   ++ +k+g++a if  L+e++invd+i+q  se    t+++++v+  ++++a ++L++
  lcl|NCBI__GCF_000166055.1:WP_013420319.1 270 AKDEAKVTVL--SIEDKPGVAASIFVPLSEANINVDMIVQNISEdgrkTDLTFTVAAAELPRALQVLRD 336
                                               **********..*******************************9999********************** PP

                                 TIGR00656 328 esgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaeka 396
                                                ++ + +++l  + d+ +vs++g+g++++ Gva+e+f+al+ k ini  is+se+kisvl+  + +e+a
  lcl|NCBI__GCF_000166055.1:WP_013420319.1 337 NQDTIRYRDLRGDTDMVKVSVIGVGMRSHAGVAAEMFQALAGKSINIQAISTSEIKISVLIGAAHTEEA 405
                                               ********************************************************************* PP

                                 TIGR00656 397 vrklhekle 405
                                               v++lh+ + 
  lcl|NCBI__GCF_000166055.1:WP_013420319.1 406 VNTLHSLFG 414
                                               *****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (418 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: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.54
//
[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