Alignments for a candidate for asp-kinase in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Chlorobaculum tepidum TLS

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate NP_661001.1 CT0095 aspartate kinase

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000006985.1:NP_661001.1
          Length = 470

 Score =  310 bits (794), Expect = 7e-89
 Identities = 192/478 (40%), Positives = 283/478 (59%), Gaps = 32/478 (6%)

Query: 4   VMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIA 63
           VMKFGGTSVGS   +R V   V ++KK    +VV+ SA S +TN L++I+  A     + 
Sbjct: 3   VMKFGGTSVGSAAAMRQVIANVAEKKKSSAPLVVL-SACSGITNKLIQIADAA-GSGCLE 60

Query: 64  KVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRD 123
           +    +  +R+ H   I E I+SEE+++EV   I+  +  LE++  G+  +GELT +S+D
Sbjct: 61  EAQQLVGEVRQFHLDLIGELIESEELQQEVIAKIEVYLTRLERLTEGIEIVGELTERSKD 120

Query: 124 YILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSAR----VKRLEVKERLL 179
              SFGE LS+ + + A+ + G     ++     +ITD+ FG AR    + +    E + 
Sbjct: 121 RFCSFGELLSTSVFAAALNEAGVSCKWIDVRTV-MITDDRFGFARPLAEICQKNTSEIIK 179

Query: 180 PLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTD 239
           PLL  G + V  G+IG TE G  TTLGRGGSD SAAL G  L ++ IEIWTDV GV TTD
Sbjct: 180 PLLDAGTVVVTQGYIGATESGRTTTLGRGGSDLSAALFGAWLHSESIEIWTDVDGVMTTD 239

Query: 240 PRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLIT 299
           PR+VP A+ I  +++ EA ELAY GAKVLHP TI PA++K IP+ V NT+ P+S+GTLIT
Sbjct: 240 PRIVPEAKSIRVMTFSEAAELAYLGAKVLHPDTIAPAVQKNIPVYVLNTWHPDSKGTLIT 299

Query: 300 NDMEM-----SDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQ 354
           ND E+        +VK+I+  K  A++NI    M G  G  + +F       ++V +IS 
Sbjct: 300 NDPELLAGKSHGGLVKSIAVKKAQAILNIRSNRMFGRHGFMSELFDVFERFGISVEMIS- 358

Query: 355 GSSETNISLVVSEEDVDKAL-KALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAG 413
            +SE ++SL V +  V + L KAL                 + +V ++  V  +SVVG  
Sbjct: 359 -TSEVSVSLTVDDAVVSEPLIKAL---------------GALGEVEIEHKVATVSVVGDN 402

Query: 414 MRGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEKT 471
           +R +KG+AG+IF ++     N++MI+QG+SE+N+  V+DE D+   V  LH +F  ++
Sbjct: 403 LRMSKGVAGRIFNSL--RNVNLRMISQGASEINVGVVVDESDVQAAVASLHCEFFAES 458


Lambda     K      H
   0.316    0.135    0.364 

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: 500
Number of extensions: 23
Number of successful extensions: 8
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: 473
Length of database: 470
Length adjustment: 33
Effective length of query: 440
Effective length of database: 437
Effective search space:   192280
Effective search space used:   192280
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: 51 (24.3 bits)

Align candidate NP_661001.1 CT0095 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (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/TIGR00657.hmm
# target sequence database:        /tmp/gapView.2951.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
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-122  395.2   5.0   2.5e-122  395.0   5.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_661001.1  CT0095 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_661001.1  CT0095 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.0   5.0  2.5e-122  2.5e-122       4     441 ..       2     455 ..       1     456 [. 0.95

  Alignments for each domain:
  == domain 1  score: 395.0 bits;  conditional E-value: 2.5e-122
                              TIGR00657   4 iVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...keliekirek 72 
                                            +V+KFGGtSvg++  +++v   v ++k++   ++VV+SA +g+T++L+++a+ + s+     ++l+ ++r+ 
  lcl|NCBI__GCF_000006985.1:NP_661001.1   2 VVMKFGGTSVGSAAAMRQVIANVAEKKKSS-APLVVLSACSGITNKLIQIADAAGSGCLeeaQQLVGEVRQF 72 
                                            9*********************99999555.9*******************99977665566999******* PP

                              TIGR00657  73 hlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvk 131
                                            hl+ + el+ s++l++++ a +e  l+ +++            er++d+  s+GE lS++++aaal+e g  
  lcl|NCBI__GCF_000006985.1:NP_661001.1  73 HLDLIGELIeSEELQQEVIAKIEVYLTRLERltegieivgeltERSKDRFCSFGELLSTSVFAAALNEAG-V 143
                                            *********9*********999999999999999************************************.9 PP

                              TIGR00657 132 avsllgaeagiltdsefgrAk....vleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAa 199
                                            + ++++ + +++td++fg A+      ++ ++e +++ll++g++vv++G+iGate+g++ttLGRGGSDl+Aa
  lcl|NCBI__GCF_000006985.1:NP_661001.1 144 SCKWIDVRTVMITDDRFGFARplaeICQKNTSEIIKPLLDAGTVVVTQGYIGATESGRTTTLGRGGSDLSAA 215
                                            *********************998667777888899************************************ PP

                              TIGR00657 200 llAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvks 271
                                            l +a l+ + +ei+tDVdG++t+DPrivpeA+ +  +++ Ea+ELa+lGakvLhp+t+ pa++++ip+ v +
  lcl|NCBI__GCF_000006985.1:NP_661001.1 216 LFGAWLHSESIEIWTDVDGVMTTDPRIVPEAKSIRVMTFSEAAELAYLGAKVLHPDTIAPAVQKNIPVYVLN 287
                                            ************************************************************************ PP

                              TIGR00657 272 tfnpeaeGTlivaksk....seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilq 337
                                            t+ p+++GTli+++ +    +++   vk+++++k qa+++++++ m    g+++e+f   ++ +++v++i+ 
  lcl|NCBI__GCF_000006985.1:NP_661001.1 288 TWHPDSKGTLITNDPEllagKSHGGLVKSIAVKKAQAILNIRSNRMFgrHGFMSELFDVFERFGISVEMIS- 358
                                            ********************9999**********************999**********************. PP

                              TIGR00657 338 sssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeenin 409
                                             +se s+s++vd+  +++   l    +k++ al+eve+e+k+a+vs+vG++++  +gva++if+ L++  +n
  lcl|NCBI__GCF_000006985.1:NP_661001.1 359 -TSEVSVSLTVDDAVVSEP--L----IKALGALGEVEIEHKVATVSVVGDNLRMSKGVAGRIFNSLRN--VN 421
                                            .88889****998766543..3....5689************************************98..9* PP

                              TIGR00657 410 iemis..sseikisvvvdekdaekavealheklv 441
                                             +mis  +sei++ vvvde+d+++av  lh +++
  lcl|NCBI__GCF_000006985.1:NP_661001.1 422 LRMISqgASEINVGVVVDESDVQAAVASLHCEFF 455
                                            *****99***********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (470 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: 10.70
//
[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