GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Thiohalospira halophila DSM 15071 HL 3

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_093427781.1 BM272_RS05535 aspartate kinase

Query= BRENDA::O69077
         (412 letters)



>NCBI__GCF_900112605.1:WP_093427781.1
          Length = 413

 Score =  587 bits (1512), Expect = e-172
 Identities = 308/409 (75%), Positives = 347/409 (84%), Gaps = 1/409 (0%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60
           MALIVQK+GGTSVGT ERIE VA++V   R AGDDVVVVVSAMSGETNRL+ LA ++  +
Sbjct: 1   MALIVQKYGGTSVGTPERIEAVADQVCARRRAGDDVVVVVSAMSGETNRLVELAGRVDPE 60

Query: 61  PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120
              RELDV+++TGEQVTIALL+MAL +R   A SYTG+QVRILTDSA+ KARIL ID  H
Sbjct: 61  ANGRELDVLLATGEQVTIALLAMALERRECEARSYTGSQVRILTDSAYNKARILDIDGEH 120

Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           +R+DL  GRVVVVAGFQG+D  G+ITTLGRGGSDTT VALAAALKADECQI+TDVDGVYT
Sbjct: 121 VRSDLGHGRVVVVAGFQGIDEAGSITTLGRGGSDTTAVALAAALKADECQIFTDVDGVYT 180

Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240
           TDPRVVP ARRL++ITFEEMLEMASLGSKVLQIRAVEFAGKY+VPLRVL SFQEGPGTLI
Sbjct: 181 TDPRVVPGARRLERITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLSSFQEGPGTLI 240

Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300
           T+D+ +  MEQP+ISGIAFNRDEAK+TIRGVPDTPG+A +ILGPI  AN+EVDMI+QNV 
Sbjct: 241 TVDEGDNDMEQPVISGIAFNRDEAKVTIRGVPDTPGIASRILGPIGDANIEVDMIIQNVG 300

Query: 301 HD-NTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVAS 359
            D  TTDFTFTVHRNDY   +EIL+  A   GARE  GD  I KVS+VGVGMRSHAG+A 
Sbjct: 301 ADGGTTDFTFTVHRNDYQRVVEILQALAEEFGAREVAGDDRIVKVSLVGVGMRSHAGIAG 360

Query: 360 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 408
            MF ALA E INIQMI+TSEIK+SVVI+EKYLEL VRALH AF L+  A
Sbjct: 361 TMFRALADEGINIQMIATSEIKISVVIDEKYLELGVRALHQAFNLEEAA 409


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: 588
Number of extensions: 18
Number of successful extensions: 3
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: 413
Length adjustment: 31
Effective length of query: 381
Effective length of database: 382
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_093427781.1 BM272_RS05535 (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.1895032.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-133  430.9   6.8   2.9e-133  430.7   6.8    1.0  1  NCBI__GCF_900112605.1:WP_093427781.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093427781.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.7   6.8  2.9e-133  2.9e-133       1     406 [.       1     405 [.       1     406 [. 0.98

  Alignments for each domain:
  == domain 1  score: 430.7 bits;  conditional E-value: 2.9e-133
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + liVqK+GGtsvg  eri+++a++v ++ + g++vvVVvSAms++t++lvela        +  e + re d
  NCBI__GCF_900112605.1:WP_093427781.1   1 MALIVQKYGGTSVGTPERIEAVADQVCARRRAGDDVVVVVSAMSGETNRLVELA------GRVDPEANGRELD 67 
                                           579***************************************************......799999******* PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                            l+++GE++++all++al++++ +a++++g +  ilTd+ +++A+i +++  e++ + L +g +vvvaGF+G 
  NCBI__GCF_900112605.1:WP_093427781.1  68 VLLATGEQVTIALLAMALERRECEARSYTGSQVRILTDSAYNKARILDIDG-EHVRSDLGHGRVVVVAGFQGI 139
                                           ***************************************************.9******************** PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                           +e G iTtLGRGGSD+tA++laaalkAd+++i+TDV+GvyttDPrvv+ a+++++i++eE+le+A+lG kvl+
  NCBI__GCF_900112605.1:WP_093427781.1 140 DEAGSITTLGRGGSDTTAVALAAALKADECQIFTDVDGVYTTDPRVVPGARRLERITFEEMLEMASLGSKVLQ 212
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.....kkensslvkaialeknvarltvegegmlgkrgilaeif 287
                                            ra+e+a +++vp++v ss+++  gTlit      ++e++ ++++ia++++ a++t++  g+ + +gi+++i 
  NCBI__GCF_900112605.1:WP_093427781.1 213 IRAVEFAGKYSVPLRVLSSFQEGPGTLITVdegdnDMEQP-VISGIAFNRDEAKVTIR--GVPDTPGIASRIL 282
                                           *****************************87888788888.*****************..9************ PP

                             TIGR00656 288 kaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglvea 356
                                           + +++++i vd+i+q  +     t+ +++v+++d ++ +++L++  ++++ +++  +  + +vs+vg+g++++
  NCBI__GCF_900112605.1:WP_093427781.1 283 GPIGDANIEVDMIIQNVGAdggtTDFTFTVHRNDYQRVVEILQALAEEFGAREVAGDDRIVKVSLVGVGMRSH 355
                                           ***************99877888************************************************** PP

                             TIGR00656 357 pGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                            G+a+ +f al++++ini mi++se+kisv++dek++e  vr+lh+++ +
  NCBI__GCF_900112605.1:WP_093427781.1 356 AGIAGTMFRALADEGINIQMIATSEIKISVVIDEKYLELGVRALHQAFNL 405
                                           **********************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (413 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.53
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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