Alignments for a candidate for asp-kinase in Methylocapsa aurea KYG T

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methylocapsa aurea KYG T

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_036262203.1 DL86_RS12820 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000746085.1:WP_036262203.1
          Length = 412

 Score =  396 bits (1018), Expect = e-115
 Identities = 224/415 (53%), Positives = 293/415 (70%), Gaps = 14/415 (3%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISG- 59
           M+ +V KFGGTSV  +ERI  VA  V++ R AG+D+ VV+SAMSG+TN L+   +  SG 
Sbjct: 1   MSRLVMKFGGTSVADIERIRNVARHVERERKAGNDIAVVVSAMSGKTNELVRWCEEASGL 60

Query: 60  -DQQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQI 118
            DQ    RE D +V++GEQVT  LLA+ L + G+PA S+ G QV ILT ++H  ARI  +
Sbjct: 61  CDQ----REYDAVVASGEQVTAGLLAIVLQEIGIPARSWQGWQVPILTSNSHGSARIAHV 116

Query: 119 DDQKIRTDLKA-GRVVVVAGFQGVD-EQGNITTLGRGGSDTTGVALAAALKADECQIYTD 176
           + + I     A G V VVAGFQG++ E G I TLGRGGSDT+ VA+AAA+ A  C IYTD
Sbjct: 117 EGRAILEGFSARGEVAVVAGFQGLNKETGRIATLGRGGSDTSAVAIAAAIGASRCDIYTD 176

Query: 177 VDGVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKE 236
           VDGVYTTDPR+V  A+RLD++ FEEMLEMASLG+KVLQ+R+VE A  + V   V  SF +
Sbjct: 177 VDGVYTTDPRIVPKAKRLDRVAFEEMLEMASLGAKVLQVRSVELAMAHKVKTFVRSSFDD 236

Query: 237 ----GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIE 292
                PGTLI  DEE+ +EQ +++GIAF+RDEA++T+R V D PGVA  I  P++ ANI 
Sbjct: 237 PRDPKPGTLI-CDEEDIVEQQVVTGIAFSRDEAQITLRQVADHPGVAAAIFMPLAEANIN 295

Query: 293 VDMIVQNVSHDN-TTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVG 351
           VDMIVQ  S D+  TD TFTV   +++  + ILQ    +IG + + G + + K+S +GVG
Sbjct: 296 VDMIVQVASEDSGATDMTFTVSTADFERTKAILQKAQPQIGFQSLNGASDVVKISAIGVG 355

Query: 352 MRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 406
           MRSHAGVA+R F+ALA++ INI+ I+TSEIK SV+IE  Y ELAVR LH+ + LD
Sbjct: 356 MRSHAGVAARAFKALAEKGINIRAITTSEIKFSVLIEAAYTELAVRTLHSLYGLD 410


Lambda     K      H
   0.316    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: 398
Number of extensions: 17
Number of successful extensions: 7
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: 413
Length of database: 412
Length adjustment: 31
Effective length of query: 382
Effective length of database: 381
Effective search space:   145542
Effective search space used:   145542
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_036262203.1 DL86_RS12820 (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.28800.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.9e-127  409.9   7.5   6.6e-127  409.8   7.5    1.0  1  lcl|NCBI__GCF_000746085.1:WP_036262203.1  DL86_RS12820 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000746085.1:WP_036262203.1  DL86_RS12820 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.8   7.5  6.6e-127  6.6e-127       4     404 ..       4     407 ..       1     410 [. 0.96

  Alignments for each domain:
  == domain 1  score: 409.8 bits;  conditional E-value: 6.6e-127
                                 TIGR00656   4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 
                                                V+KFGGtsv+++eri+++a++v +e k g++  VVvSAms++t+elv         e  s    +re 
  lcl|NCBI__GCF_000746085.1:WP_036262203.1   4 LVMKFGGTSVADIERIRNVARHVERERKAGNDIAVVVSAMSGKTNELVRWC------EEASGLCDQREY 66 
                                               69*************************************************......7999999***** PP

                                 TIGR00656  73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141
                                               d +v+ GE++++ ll+ +l+e g  a++ +g++ +ilT++++g+A+i +++ +  L+   ++g + vva
  lcl|NCBI__GCF_000746085.1:WP_036262203.1  67 DAVVASGEQVTAGLLAIVLQEIGIPARSWQGWQVPILTSNSHGSARIAHVEGRAILEGFSARGEVAVVA 135
                                               ****************************************************888888999******** PP

                                 TIGR00656 142 GFiGat.eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209
                                               GF+G + e G+i tLGRGGSD++A+++aaa+ A+r++iyTDV+GvyttDPr+v++ak++d++++eE+le
  lcl|NCBI__GCF_000746085.1:WP_036262203.1 136 GFQGLNkETGRIATLGRGGSDTSAVAIAAAIGASRCDIYTDVDGVYTTDPRIVPKAKRLDRVAFEEMLE 204
                                               ****76267************************************************************ PP

                                 TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsske....keegTlitn..kkensslvkaialeknvarltve 272
                                               +A+lGakvl+ r++ela++ kv+ +vrss++    ++ gTli++  +  ++++v++ia++++ a++t++
  lcl|NCBI__GCF_000746085.1:WP_036262203.1 205 MASLGAKVLQVRSVELAMAHKVKTFVRSSFDdprdPKPGTLICDeeDIVEQQVVTGIAFSRDEAQITLR 273
                                               *****************************863322569*****966555668***************** PP

                                 TIGR00656 273 gegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesl 337
                                                 ++++++g++a if  Lae++invd+i+q  se    t+++++v++ d +++k++L++ + +++++sl
  lcl|NCBI__GCF_000746085.1:WP_036262203.1 274 --QVADHPGVAAAIFMPLAEANINVDMIVQVASEdsgaTDMTFTVSTADFERTKAILQKAQPQIGFQSL 340
                                               ..******************************999999******************************* PP

                                 TIGR00656 338 eveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404
                                               +  +d+ ++s++g+g++++ Gva+++fkal+ek+ini  i++se+k svl++ +++e avr+lh+ +
  lcl|NCBI__GCF_000746085.1:WP_036262203.1 341 NGASDVVKISAIGVGMRSHAGVAARAFKALAEKGINIRAITTSEIKFSVLIEAAYTELAVRTLHSLY 407
                                               ****************************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (412 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.14
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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