GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Streptacidiphilus oryzae TH49

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_037574568.1 BS73_RS20470 aspartate kinase

Query= BRENDA::P9WPX3
         (421 letters)



>NCBI__GCF_000744815.1:WP_037574568.1
          Length = 425

 Score =  550 bits (1418), Expect = e-161
 Identities = 282/425 (66%), Positives = 349/425 (82%), Gaps = 4/425 (0%)

Query: 1   MALVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPA 60
           M LVVQKYGGSSVADAE I+RVA RIV TKK G++VVVVVSAMGDTTD+L+DLA++V P 
Sbjct: 1   MGLVVQKYGGSSVADAEGIKRVARRIVDTKKAGHEVVVVVSAMGDTTDELIDLAEEVSPI 60

Query: 61  PPPRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGR 120
           P  RELDMLLTAGERIS AL+AMAI+SLG  A+SFTGSQAGVIT   H  A+IIDVTPGR
Sbjct: 61  PGGRELDMLLTAGERISMALLAMAIKSLGHEAQSFTGSQAGVITDSVHNKARIIDVTPGR 120

Query: 121 LQTALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIF 180
           ++T+L+EG + +VAGFQGVSQD+K++TTLGRGGSDTTAVA+AAAL A+VCEIYTDVDG+F
Sbjct: 121 IRTSLDEGNIAIVAGFQGVSQDSKNITTLGRGGSDTTAVALAAALDAEVCEIYTDVDGVF 180

Query: 181 SADPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTV 240
           +ADPR+V+ ARK+D + FE+MLE+A+ G+KVL+ RCVEYARR+NIP+HVRSS+S   GT 
Sbjct: 181 TADPRVVKKARKIDEIAFEDMLELASSGSKVLLHRCVEYARRYNIPIHVRSSFSGLQGTW 240

Query: 241 VVGSIKD---VPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDMVL 297
           V    +      ME  I++GVAHD SEAK+T+VG+PD PG AA++FRA+ADA++NIDMV+
Sbjct: 241 VRNKEESEGAAEMEQAIISGVAHDTSEAKITVVGVPDKPGEAARIFRAIADAEINIDMVV 300

Query: 298 QNVSKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMRSH 357
           QNVS+     TDI+FT  +  G  A+E L+ ++  IG+  L YDD IGK+SL+GAGMRS+
Sbjct: 301 QNVSQATTSLTDISFTLPKTEGRKAIEALEKVQAGIGYDSLRYDDQIGKISLVGAGMRSN 360

Query: 358 PGVTATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGD-EEATVY 416
           PGVTATF EAL+  GVNIELISTSEIRISV+ R  ++++AV A+H AFGL  D +EA VY
Sbjct: 361 PGVTATFFEALSNAGVNIELISTSEIRISVVTRADDVNQAVQAVHSAFGLDSDSDEAVVY 420

Query: 417 AGTGR 421
            GTGR
Sbjct: 421 GGTGR 425


Lambda     K      H
   0.318    0.134    0.376 

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: 506
Number of extensions: 15
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: 421
Length of database: 425
Length adjustment: 32
Effective length of query: 389
Effective length of database: 393
Effective search space:   152877
Effective search space used:   152877
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_037574568.1 BS73_RS20470 (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.815660.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-129  417.9  12.9   2.5e-129  417.7  12.9    1.0  1  NCBI__GCF_000744815.1:WP_037574568.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037574568.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.7  12.9  2.5e-129  2.5e-129       1     405 [.       1     409 [.       1     411 [. 0.97

  Alignments for each domain:
  == domain 1  score: 417.7 bits;  conditional E-value: 2.5e-129
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + l+VqK+GG+sv++ e+ik++a+++++++k g++vvVVvSAm+ +tdel++la      e +s  +  re d
  NCBI__GCF_000744815.1:WP_037574568.1   1 MGLVVQKYGGSSVADAEGIKRVARRIVDTKKAGHEVVVVVSAMGDTTDELIDLA------EEVSPIPGGRELD 67 
                                           579***************************************************......799********** PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           +l+  GE++s+all++a++ lg++a++++g +ag++Td+ +++A+i ++ +  r+   L+eg i +vaGF+G 
  NCBI__GCF_000744815.1:WP_037574568.1  68 MLLTAGERISMALLAMAIKSLGHEAQSFTGSQAGVITDSVHNKARIIDVTP-GRIRTSLDEGNIAIVAGFQGV 139
                                           ***************************************************.********************9 PP

                             TIGR00656 147 teeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvl 218
                                            ++  +iTtLGRGGSD+tA++laaal+A+ +eiyTDV+Gv+t+DPrvv++a+kid+i++e++lelA+ G kvl
  NCBI__GCF_000744815.1:WP_037574568.1 140 SQDSkNITTLGRGGSDTTAVALAAALDAEVCEIYTDVDGVFTADPRVVKKARKIDEIAFEDMLELASSGSKVL 212
                                           888736******************************************************************* PP

                             TIGR00656 219 hpralelaveakvpilvrsskekeegTlitn........kkensslvkaialeknvarltvegegmlgkrgil 283
                                             r +e+a ++++pi vrss++  +gT + n        ++e+  +++++a++   a++tv+  g+ +k+g +
  NCBI__GCF_000744815.1:WP_037574568.1 213 LHRCVEYARRYNIPIHVRSSFSGLQGTWVRNkeesegaaEMEQA-IISGVAHDTSEAKITVV--GVPDKPGEA 282
                                           *******************************7777776555555.*****************..9******** PP

                             TIGR00656 284 aeifkaLaeeeinvdlisqtese.....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivga 351
                                           a+if a+a++ein+d+++q  s+     t+is+++ +++  +a +aL++++  ++++sl ++ ++ ++s+vga
  NCBI__GCF_000744815.1:WP_037574568.1 283 ARIFRAIADAEINIDMVVQNVSQattslTDISFTLPKTEGRKAIEALEKVQAGIGYDSLRYDDQIGKISLVGA 355
                                           ******************9988888889********************************************* PP

                             TIGR00656 352 glveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                           g++++pGv++  f+al++ ++ni  is+se++isv+ +  d+++av+++h+++ 
  NCBI__GCF_000744815.1:WP_037574568.1 356 GMRSNPGVTATFFEALSNAGVNIELISTSEIRISVVTRADDVNQAVQAVHSAFG 409
                                           ***************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (425 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: 00:00:00.00
# Mc/sec: 21.01
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

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:

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