Alignments for a candidate for asp-kinase in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Sinorhizobium medicae WSM419

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate YP_001328169.1 Smed_2504 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>NCBI__GCF_000017145.1:YP_001328169.1
          Length = 424

 Score =  389 bits (1000), Expect = e-113
 Identities = 217/423 (51%), Positives = 290/423 (68%), Gaps = 18/423 (4%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAK---AI 57
           MA IV KFGGTSV  + RI  VA  VK+  DAG ++ VV+SAMSG+TN L+   +    +
Sbjct: 1   MARIVMKFGGTSVADLNRIHNVARHVKREVDAGHEVAVVVSAMSGKTNELVGWVENMPKV 60

Query: 58  SGDQQPL--PRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARI 115
           +G   P    RE D +V++GEQVT  LLA+AL   G+ A S+ G Q+ I TD+AH  ARI
Sbjct: 61  AGSNAPFYDAREYDAVVASGEQVTSGLLAIALQSMGINARSWQGWQLPIRTDNAHGAARI 120

Query: 116 LQIDDQKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYT 175
           L ID   I   +  G+V VVAGFQG+     + TLGRGGSDT+ VA+AAA+KAD C IYT
Sbjct: 121 LDIDGTDITRRMGEGQVAVVAGFQGLGPDNRLATLGRGGSDTSAVAIAAAVKADRCDIYT 180

Query: 176 DVDGVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFK 235
           DVDGVYTTDPR+   A+RL KI FEEMLEMASLG+KVLQ+R+VE A  + V   V  SF+
Sbjct: 181 DVDGVYTTDPRIEPKARRLKKIAFEEMLEMASLGAKVLQVRSVELAMVHKVRTFVRSSFE 240

Query: 236 E-----------GPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILG 284
           +            PGTLI  DE+E +EQ +++GIA+ +DEA++++R + D PGV+  I G
Sbjct: 241 DPDAPGMGDLMNPPGTLI-CDEDEIVEQEVVTGIAYAKDEAQISLRRLADRPGVSAAIFG 299

Query: 285 PISGANIEVDMIVQNVSHDNT-TDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIA 343
           P++ A+I VDMIVQN+S D + TD TFTV   + D A R+L +  ++IG   +  ++ + 
Sbjct: 300 PLAEAHINVDMIVQNISEDGSKTDMTFTVPSGDVDKALRVLGDNKEKIGYDVIQSESGLV 359

Query: 344 KVSIVGVGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAF 403
           KVS++G+GMRSHAGVA+  F ALA + INI+ I+TSEIK+S++I+  Y ELAVR LH+ +
Sbjct: 360 KVSVIGIGMRSHAGVAASAFRALADKGINIKAITTSEIKISILIDGPYAELAVRTLHSTY 419

Query: 404 ELD 406
            LD
Sbjct: 420 GLD 422


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: 460
Number of extensions: 21
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: 413
Length of database: 424
Length adjustment: 32
Effective length of query: 381
Effective length of database: 392
Effective search space:   149352
Effective search space used:   149352
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 YP_001328169.1 Smed_2504 (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.2969.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-129  417.5   3.2   3.6e-129  417.2   3.2    1.1  1  lcl|NCBI__GCF_000017145.1:YP_001328169.1  Smed_2504 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017145.1:YP_001328169.1  Smed_2504 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.2   3.2  3.6e-129  3.6e-129       3     405 ..       3     420 ..       1     422 [. 0.94

  Alignments for each domain:
  == domain 1  score: 417.2 bits;  conditional E-value: 3.6e-129
                                 TIGR00656   3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdei...s 68 
                                                iV+KFGGtsv++ +ri+++a++v++e+  g++v VVvSAms++t+elv  +e  ++ ++  ++     
  lcl|NCBI__GCF_000017145.1:YP_001328169.1   3 RIVMKFGGTSVADLNRIHNVARHVKREVDAGHEVAVVVSAMSGKTNELVGWVE--NMPKVAGSNApfyD 69 
                                               59**************************************************8..55444444434559 PP

                                 TIGR00656  69 prerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegii 137
                                                re d +v+ GE+++s ll+ al+  g +a++ +g++ +i+Td+ +g A+i +++    ++ ++ eg++
  lcl|NCBI__GCF_000017145.1:YP_001328169.1  70 AREYDAVVASGEQVTSGLLAIALQSMGINARSWQGWQLPIRTDNAHGAARILDIDG-TDITRRMGEGQV 137
                                               *******************************************************9.9*********** PP

                                 TIGR00656 138 vvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeE 206
                                                vvaGF+G   + +  tLGRGGSD++A+++aaa+kAdr++iyTDV+GvyttDPr+ ++a++++ki++eE
  lcl|NCBI__GCF_000017145.1:YP_001328169.1 138 AVVAGFQGLGPDNRLATLGRGGSDTSAVAIAAAVKADRCDIYTDVDGVYTTDPRIEPKARRLKKIAFEE 206
                                               ********************************************************************* PP

                                 TIGR00656 207 alelAtlGakvlhpralelaveakvpilvrsske..........ke.egTlitn..kkensslvkaial 262
                                               +le+A+lGakvl+ r++ela+  kv  +vrss+e           +  gTli++  +  ++++v++ia+
  lcl|NCBI__GCF_000017145.1:YP_001328169.1 207 MLEMASLGAKVLQVRSVELAMVHKVRTFVRSSFEdpdapgmgdlMNpPGTLICDedEIVEQEVVTGIAY 275
                                               ********************************973333333332244799**9955444558******* PP

                                 TIGR00656 263 eknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLke 327
                                                k+ a+++++   +++++g+ a if+ Lae++invd+i+q  se    t+++++v   dvd+a ++L +
  lcl|NCBI__GCF_000017145.1:YP_001328169.1 276 AKDEAQISLR--RLADRPGVSAAIFGPLAEAHINVDMIVQNISEdgskTDMTFTVPSGDVDKALRVLGD 342
                                               **********..******************************999999********************* PP

                                 TIGR00656 328 esgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaeka 396
                                                +++++++ ++ e++l +vs++g g++++ Gva+ +f al++k+ini+ i++se+kis+l+d+ +ae a
  lcl|NCBI__GCF_000017145.1:YP_001328169.1 343 NKEKIGYDVIQSESGLVKVSVIGIGMRSHAGVAASAFRALADKGINIKAITTSEIKISILIDGPYAELA 411
                                               ********************************************************************* PP

                                 TIGR00656 397 vrklhekle 405
                                               vr+lh+++ 
  lcl|NCBI__GCF_000017145.1:YP_001328169.1 412 VRTLHSTYG 420
                                               *****9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (424 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.

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