Alignments for a candidate for asp-kinase in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_068174296.1 HTA01S_RS18935 aspartate kinase

Query= SwissProt::Q88EI9
         (411 letters)



>NCBI__GCF_001592305.1:WP_068174296.1
          Length = 426

 Score =  514 bits (1325), Expect = e-150
 Identities = 269/418 (64%), Positives = 331/418 (79%), Gaps = 14/418 (3%)

Query: 1   MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQI--- 57
           MALIV K+GGTS+GS ERI  VA +V K  +AG  +VVV SAMSGETNRL+ LAK++   
Sbjct: 1   MALIVHKYGGTSMGSTERIRNVARRVAKWHKAGHQMVVVPSAMSGETNRLLGLAKELAPA 60

Query: 58  -TDQPVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQI 116
            TD    RELD++ +TGEQ + ALL +AL   G+ AVSY G QV I T+S++ KARI  I
Sbjct: 61  KTDSAYGRELDMLAATGEQASSALLAIALQAEGLEAVSYAGWQVPIKTNSAYTKARIESI 120

Query: 117 DDQKIRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVD 176
           DD ++RADL  G+VV+V GFQGVD  G+ITTLGRGGSDT+ VA+AAALKA EC IYTDVD
Sbjct: 121 DDARVRADLGAGKVVIVTGFQGVDPEGNITTLGRGGSDTSAVAVAAALKAAECLIYTDVD 180

Query: 177 GVYTTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSF---- 232
           GVYTTDPRVVP+ARRL +++FEEMLEMAS+GSKVLQIRSVEFAGKY VPLRVL SF    
Sbjct: 181 GVYTTDPRVVPEARRLLRVSFEEMLEMASMGSKVLQIRSVEFAGKYKVPLRVLSSFTPWD 240

Query: 233 -----KEGPGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAS 287
                +   GTLIT +E+E MEQ ++SGIAFNRDEAK+++ GVPD PG+A++ILG ++ +
Sbjct: 241 IDLNEEAASGTLITFEEDEEMEQAVVSGIAFNRDEAKISVLGVPDKPGIAYQILGAVAEA 300

Query: 288 NIEVDMIVQNVAHDNTTDFTFTVHRNEYEKAQSVLEN-TAREIGAREVIGDTKIAKVSIV 346
           NIEVD+I+QN++ D  TDF+FTVHR E++KA  +L+N    E+GA +V+GD +I KVSIV
Sbjct: 301 NIEVDVIIQNLSKDGKTDFSFTVHRGEFQKAMDLLKNKVVPELGAADVVGDARICKVSIV 360

Query: 347 GVGMRSHAGVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404
           G+GMRSH GVAS MF+ L+ E INIQMISTSEIK SVV++EKY+ELAVRALH  FDLD
Sbjct: 361 GIGMRSHVGVASRMFKCLSDEGINIQMISTSEIKTSVVIDEKYMELAVRALHREFDLD 418


Lambda     K      H
   0.316    0.133    0.358 

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: 529
Number of extensions: 14
Number of successful extensions: 4
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: 411
Length of database: 426
Length adjustment: 32
Effective length of query: 379
Effective length of database: 394
Effective search space:   149326
Effective search space used:   149326
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_068174296.1 HTA01S_RS18935 (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.1401876.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-128  415.2   5.3   1.7e-128  415.0   5.3    1.0  1  NCBI__GCF_001592305.1:WP_068174296.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001592305.1:WP_068174296.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.0   5.3  1.7e-128  1.7e-128       1     406 [.       1     417 [.       1     418 [. 0.95

  Alignments for each domain:
  == domain 1  score: 415.0 bits;  conditional E-value: 1.7e-128
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + liV K+GGts+gs+eri+++a++v k  k g+++vVV SAms++t++l+ la   +l+ a+ d    re d
  NCBI__GCF_001592305.1:WP_068174296.1   1 MALIVHKYGGTSMGSTERIRNVARRVAKWHKAGHQMVVVPSAMSGETNRLLGLA--KELAPAKTDSAYGRELD 71 
                                           579***************************************************..69*************** PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           +l ++GE+ ssall+ al+++g +a+++ g++ +i T++ +++A+i++++   r+   L  g++v+v+GF+G 
  NCBI__GCF_001592305.1:WP_068174296.1  72 MLAATGEQASSALLAIALQAEGLEAVSYAGWQVPIKTNSAYTKARIESIDD-ARVRADLGAGKVVIVTGFQGV 143
                                           **************************************************9.9******************** PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                           + eG+iTtLGRGGSD++A+++aaalkA ++ iyTDV+GvyttDPrvv+ea+++ ++s+eE+le+A++G kvl+
  NCBI__GCF_001592305.1:WP_068174296.1 144 DPEGNITTLGRGGSDTSAVAVAAALKAAECLIYTDVDGVYTTDPRVVPEARRLLRVSFEEMLEMASMGSKVLQ 216
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrssk........eke.egTlitn....kkensslvkaialeknvarltvegegmlgk 279
                                            r++e+a ++kvp++v ss+        e+  +gTlit     ++e+  +v++ia++++ a+++v   g+ +k
  NCBI__GCF_001592305.1:WP_068174296.1 217 IRSVEFAGKYKVPLRVLSSFtpwdidlnEEAaSGTLITFeedeEMEQ-AVVSGIAFNRDEAKISVL--GVPDK 286
                                           ******************973333333222358****9866545555.5*****************..9**** PP

                             TIGR00656 280 rgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesg.aaelesleveedlavvsi 348
                                           +gi+ +i +a+ae++i vd+i+q  s+   t+ s++v++ + ++a ++Lk+++  +++  ++  +  +++vsi
  NCBI__GCF_001592305.1:WP_068174296.1 287 PGIAYQILGAVAEANIEVDVIIQNLSKdgkTDFSFTVHRGEFQKAMDLLKNKVVpELGAADVVGDARICKVSI 359
                                           ***********************9988888*******************98864256799************* PP

                             TIGR00656 349 vgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           vg g++++ Gvas++fk l++++ini mis+se+k sv++dek++e avr+lh+++ +
  NCBI__GCF_001592305.1:WP_068174296.1 360 VGIGMRSHVGVASRMFKCLSDEGINIQMISTSEIKTSVVIDEKYMELAVRALHREFDL 417
                                           *******************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (426 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: 14.15
//
[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:

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