Alignments for a candidate for asp-kinase in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Thermus aquaticus YT-1

Align Aspartokinase; Aspartate kinase; AK; ASK; Threonine-sensitive AK; ThrA; EC 2.7.2.4 (characterized)
to candidate WP_053768520.1 BVI061214_RS11775 aspartate kinase

Query= SwissProt::P61489
         (405 letters)



>NCBI__GCF_001280255.1:WP_053768520.1
          Length = 405

 Score =  754 bits (1948), Expect = 0.0
 Identities = 387/405 (95%), Positives = 397/405 (98%)

Query: 1   MALVVQKYGGTSVGDLERIHKVAQRIAHYREKGHRLAVVVSAMGHTTDELIALAKRVNPR 60
           MALVVQKYGGTSVGDLERIHKVAQRIAHYREKGHRLAVVVSAMGHTTDELIALAKRVNPR
Sbjct: 1   MALVVQKYGGTSVGDLERIHKVAQRIAHYREKGHRLAVVVSAMGHTTDELIALAKRVNPR 60

Query: 61  PPFRELDLLTTTGEQVSVALLSMQLWAMGIPAKGFVQHQIGITTDGRYGDARILEVNPAR 120
           PPFRELDLLTTTGEQVSVALLSMQLWAMGIPAKGFVQHQIGI TDGRYGDARILEV+P+R
Sbjct: 61  PPFRELDLLTTTGEQVSVALLSMQLWAMGIPAKGFVQHQIGIKTDGRYGDARILEVDPSR 120

Query: 121 IREALDQGFVAVIAGFMGTTPEGEITTLGRGGSDTTAVAIAAALGAKECEIYTDTEGVYT 180
           I +ALD+G+VAVIAGFMGTT EGEITTLGRGGSDTTAVAIAAALGAKECEIYTDTEGVYT
Sbjct: 121 IVKALDEGYVAVIAGFMGTTEEGEITTLGRGGSDTTAVAIAAALGAKECEIYTDTEGVYT 180

Query: 181 TDPHLIPEARKLSVIGYDQMLEMAALGARVLHPRAVYYAKRYGVVLHVRSSFSYNPGTLV 240
           TDPHLIPEARKL VIGYDQMLEMAALGARVLHPRAVYYAKRYGVVLHVRSSFSYNPGTLV
Sbjct: 181 TDPHLIPEARKLEVIGYDQMLEMAALGARVLHPRAVYYAKRYGVVLHVRSSFSYNPGTLV 240

Query: 241 KEVAMEMDKAVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGHD 300
           KEV+MEM K VTG ALDLDHAQIGLIGIPDQPGIAAKVFQALA+RGIAVDMIIQGVPGHD
Sbjct: 241 KEVSMEMGKTVTGAALDLDHAQIGLIGIPDQPGIAAKVFQALADRGIAVDMIIQGVPGHD 300

Query: 301 PSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMF 360
           PSRQQMAFTVKKDFAQEALEALEPVLAEIGGEA+LRPDIAKVSIVGVGLAS PE+PAKMF
Sbjct: 301 PSRQQMAFTVKKDFAQEALEALEPVLAEIGGEALLRPDIAKVSIVGVGLASAPEIPAKMF 360

Query: 361 QAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFELDKA 405
           QAVASTGANIEMIATSEVRISVIIPA+YAEAALRAVHQAFELDKA
Sbjct: 361 QAVASTGANIEMIATSEVRISVIIPAQYAEAALRAVHQAFELDKA 405


Lambda     K      H
   0.319    0.135    0.379 

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: 695
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: 405
Length of database: 405
Length adjustment: 31
Effective length of query: 374
Effective length of database: 374
Effective search space:   139876
Effective search space used:   139876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_053768520.1 BVI061214_RS11775 (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.39631.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-127  409.7   0.7   7.7e-127  409.6   0.7    1.0  1  NCBI__GCF_001280255.1:WP_053768520.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053768520.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.6   0.7  7.7e-127  7.7e-127       1     406 [.       1     402 [.       1     403 [. 0.97

  Alignments for each domain:
  == domain 1  score: 409.6 bits;  conditional E-value: 7.7e-127
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           + l+VqK+GGtsvg+ eri+k+a+++ +  ++g++  VVvSAm+++tdel++la      + ++  +  re d
  NCBI__GCF_001280255.1:WP_053768520.1   1 MALVVQKYGGTSVGDLERIHKVAQRIAHYREKGHRLAVVVSAMGHTTDELIALA------KRVNPRPPFRELD 67 
                                           579***************************************************......89999******** PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                           +l  +GE++s+alls+ l + g  a+ +  ++ gi Td+++g+A+i e+++ +r+++ L+eg++ v+aGF+G+
  NCBI__GCF_001280255.1:WP_053768520.1  68 LLTTTGEQVSVALLSMQLWAMGIPAKGFVQHQIGIKTDGRYGDARILEVDP-SRIVKALDEGYVAVIAGFMGT 139
                                           ***************************************************.********************* PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                           teeGeiTtLGRGGSD+tA+++aaal A+++eiyTD eGvyttDP +++ea+k++ i y+ +le+A lGa+vlh
  NCBI__GCF_001280255.1:WP_053768520.1 140 TEEGEITTLGRGGSDTTAVAIAAALGAKECEIYTDTEGVYTTDPHLIPEARKLEVIGYDQMLEMAALGARVLH 212
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrsskekeegTlitn.kkensslvkaialeknvarltvegegmlgkrgilaeifkaLa 291
                                           pra+ +a++++v + vrss++ + gTl+ + ++e+ + v++ al+ + a++ +   g+ +++gi+a++f+aLa
  NCBI__GCF_001280255.1:WP_053768520.1 213 PRAVYYAKRYGVVLHVRSSFSYNPGTLVKEvSMEMGKTVTGAALDLDHAQIGLI--GIPDQPGIAAKVFQALA 283
                                           ******************************999999******************..9**************** PP

                             TIGR00656 292 eeeinvdlisqt.....esetsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGv 359
                                           +++i vd+i+q+     +s+++++++v++  ++ea +aL+ +  +++  +  ++ d+a+vsivg+gl +ap +
  NCBI__GCF_001280255.1:WP_053768520.1 284 DRGIAVDMIIQGvpghdPSRQQMAFTVKKDFAQEALEALEPVLAEIG-GEALLRPDIAKVSIVGVGLASAPEI 355
                                           ***********844333467**********************99998.5666788****************** PP

                             TIGR00656 360 aseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                            +++f+a++ +++ni mi++se++isv+++ ++ae a r++h+++e+
  NCBI__GCF_001280255.1:WP_053768520.1 356 PAKMFQAVASTGANIEMIATSEVRISVIIPAQYAEAALRAVHQAFEL 402
                                           *********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (405 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: 20.97
//
[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