Alignments for a candidate for asp-kinase in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pseudarthrobacter sulfonivorans Ar51

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_058930163.1 AU252_RS07410 aspartate kinase

Query= BRENDA::P9WPX3
         (421 letters)



>NCBI__GCF_001484605.1:WP_058930163.1
          Length = 452

 Score =  526 bits (1356), Expect = e-154
 Identities = 268/426 (62%), Positives = 342/426 (80%), Gaps = 7/426 (1%)

Query: 3   LVVQKYGGSSVADAERIRRVAERIVATKKQGNDVVVVVSAMGDTTDDLLDLAQQVCPAPP 62
           L+VQK+GGSSV+DAE ++RVA+R+V  ++ GN+VVVVVSAMGDTTD+LLDLA QV  + P
Sbjct: 27  LIVQKFGGSSVSDAEGVKRVAKRVVDAQRAGNEVVVVVSAMGDTTDELLDLAAQVTDSAP 86

Query: 63  PRELDMLLTAGERISNALVAMAIESLGAHARSFTGSQAGVITTGTHGNAKIIDVTPGRLQ 122
            RE+DMLL+AGERIS AL+AMAI   GA A+SFTGSQAG+IT G HG A+IIDV P R++
Sbjct: 87  AREMDMLLSAGERISMALLAMAINKFGASAQSFTGSQAGMITDGIHGKARIIDVDPHRIR 146

Query: 123 TALEEGRVVLVAGFQGVSQDTKDVTTLGRGGSDTTAVAMAAALGADVCEIYTDVDGIFSA 182
           TAL++G + +VAGFQG+S+ T ++TTLGRGGSDTTAVA+AAAL ADVCEIYTDVDGI++A
Sbjct: 147 TALDKGHIAIVAGFQGMSRSTNEITTLGRGGSDTTAVALAAALDADVCEIYTDVDGIYTA 206

Query: 183 DPRIVRNARKLDTVTFEEMLEMAACGAKVLMLRCVEYARRHNIPVHVRSSYSDRPGTVVV 242
           DPR+V +A+K+DT++ EEMLE+AA GAK+L LRCVEYARR  +P+HVRSS+S   GT V+
Sbjct: 207 DPRVVPSAQKIDTISSEEMLELAASGAKILHLRCVEYARRFGVPLHVRSSFSQNEGTWVI 266

Query: 243 GSIKD-------VPMEDPILTGVAHDRSEAKVTIVGLPDIPGYAAKVFRAVADADVNIDM 295
            S +D       V +E PI++GVAHDRSEAKVT+VG+PDIPG AA +F+ +ADA  NIDM
Sbjct: 267 PSAEDKITTQEGVALEQPIISGVAHDRSEAKVTVVGVPDIPGKAAAIFQVIADAHSNIDM 326

Query: 296 VLQNVSKVEDGKTDITFTCSRDVGPAAVEKLDSLRNEIGFSQLLYDDHIGKVSLIGAGMR 355
           ++QNVS    G+TDI+FT     G  A+E L + + +IGF  + Y++ IGK+SLIGAGMR
Sbjct: 327 IVQNVSTHGTGRTDISFTLPIVEGAEALEALKAAQPDIGFENIEYNEQIGKLSLIGAGMR 386

Query: 356 SHPGVTATFCEALAAVGVNIELISTSEIRISVLCRDTELDKAVVALHEAFGLGGDEEATV 415
           SHPGV+ATF +AL+  G+NI +ISTSEIRISV+     LD AV A+H+AF L  ++EATV
Sbjct: 387 SHPGVSATFFKALSDAGININMISTSEIRISVVTHADLLDDAVRAIHKAFDLDSEDEATV 446

Query: 416 YAGTGR 421
           Y GTGR
Sbjct: 447 YGGTGR 452


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: 503
Number of extensions: 14
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: 421
Length of database: 452
Length adjustment: 32
Effective length of query: 389
Effective length of database: 420
Effective search space:   163380
Effective search space used:   163380
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: 51 (24.3 bits)

Align candidate WP_058930163.1 AU252_RS07410 (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.23634.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-128  415.6   9.5   1.3e-128  415.4   9.5    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058930163.1  AU252_RS07410 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058930163.1  AU252_RS07410 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.4   9.5  1.3e-128  1.3e-128       2     406 ..      26     438 ..      25     439 .. 0.96

  Alignments for each domain:
  == domain 1  score: 415.4 bits;  conditional E-value: 1.3e-128
                                 TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispr 70 
                                               +liVqKFGG+sv + e++k++ak+v+++ + g++vvVVvSAm+ +tdel++la      +++ d    r
  lcl|NCBI__GCF_001484605.1:WP_058930163.1  26 QLIVQKFGGSSVSDAEGVKRVAKRVVDAQRAGNEVVVVVSAMGDTTDELLDLA------AQVTDSAPAR 88 
                                               79***************************************************......89999999** PP

                                 TIGR00656  71 erdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivv 139
                                               e+d+l+s GE++s+all++a+++ g  a++++g +ag++Td+ +g+A+i ++++ +r+   L++g i +
  lcl|NCBI__GCF_001484605.1:WP_058930163.1  89 EMDMLLSAGERISMALLAMAINKFGASAQSFTGSQAGMITDGIHGKARIIDVDP-HRIRTALDKGHIAI 156
                                               ******************************************************.************** PP

                                 TIGR00656 140 vaGFiGateeG.eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207
                                               vaGF+G+ +   eiTtLGRGGSD+tA++laaal+Ad +eiyTDV+G+yt+DPrvv++a+kid+is eE+
  lcl|NCBI__GCF_001484605.1:WP_058930163.1 157 VAGFQGMSRSTnEITTLGRGGSDTTAVALAAALDADVCEIYTDVDGIYTADPRVVPSAQKIDTISSEEM 225
                                               ******9986538******************************************************** PP

                                 TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitn............kkensslvkaialek 264
                                               lelA  Gak+lh r +e+a + +vp+ vrss++++egT +++              e+ ++++++a+++
  lcl|NCBI__GCF_001484605.1:WP_058930163.1 226 LELAASGAKILHLRCVEYARRFGVPLHVRSSFSQNEGTWVIPsaedkittqegvALEQ-PIISGVAHDR 293
                                               *****************************************97777666554444444.6********* PP

                                 TIGR00656 265 nvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese.....tsislvvdeedvdeakkaLkee 328
                                                 a++tv+  g+ + +g +a if+++a+++ n+d+i+q  s      t+is+++   +  ea +aLk+ 
  lcl|NCBI__GCF_001484605.1:WP_058930163.1 294 SEAKVTVV--GVPDIPGKAAAIFQVIADAHSNIDMIVQNVSThgtgrTDISFTLPIVEGAEALEALKAA 360
                                               ********..99*************************9877667777********************** PP

                                 TIGR00656 329 sgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekav 397
                                               + ++++e++e++e++ ++s++gag++++pGv +  fkal++ +ini mis+se++isv+ +   + +av
  lcl|NCBI__GCF_001484605.1:WP_058930163.1 361 QPDIGFENIEYNEQIGKLSLIGAGMRSHPGVSATFFKALSDAGININMISTSEIRISVVTHADLLDDAV 429
                                               ********************************************************************* PP

                                 TIGR00656 398 rklheklee 406
                                               r++h+++ +
  lcl|NCBI__GCF_001484605.1:WP_058930163.1 430 RAIHKAFDL 438
                                               *****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (452 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: 00:00:00.02
# Mc/sec: 8.23
//
[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