Alignments for a candidate for asp-kinase in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methanosarcina acetivorans C2A

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011020190.1 MA_RS00690 aspartate kinase, monofunctional class

Query= BRENDA::Q57991
         (473 letters)



>NCBI__GCF_000007345.1:WP_011020190.1
          Length = 472

 Score =  464 bits (1194), Expect = e-135
 Identities = 243/469 (51%), Positives = 333/469 (71%), Gaps = 11/469 (2%)

Query: 1   MTTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVR 60
           M  VMKFGGTSVG G++IRHVA+++ +  +E + +VVV SA+  VT+ L+E ++ A    
Sbjct: 1   MKIVMKFGGTSVGDGKKIRHVAQLLKRYHEEGNQIVVVTSALGGVTDRLLENARLASTKG 60

Query: 61  DIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPK 120
            ++ V +F   +  KH++A+++AI+   + +EV +++D RIEELEK LIG+ YLGELT +
Sbjct: 61  KVSLVKEFKTELTNKHHEAVKDAIEDPRVAKEVLQVLDLRIEELEKALIGICYLGELTSR 120

Query: 121 SRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARV--KRLEVKERL 178
           S DYI S+GERL++PI+SGA+R LG  SI   GGEAGI+T +++G+AR   K  E+  + 
Sbjct: 121 SIDYISSYGERLAAPIVSGAVRSLGAASIEYTGGEAGIVTTSDYGNARPLEKTYELVLKR 180

Query: 179 LPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTT 238
           L    E  I VVTGFIG  E+G ITTLGR GSD+SA+++G  L AD I +W +V+G+ TT
Sbjct: 181 LGCRLESHILVVTGFIGENEDGIITTLGRSGSDFSASILGAALKADEIWLWKEVNGIMTT 240

Query: 239 DPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLI 298
           DPR+VP A+ IP++SY EAMEL+YFGA VLHPRTIEPAM + IP+ VKNTF PE  GTL+
Sbjct: 241 DPRIVPEAKTIPQISYAEAMELSYFGANVLHPRTIEPAMREHIPVRVKNTFNPEFPGTLV 300

Query: 299 TNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSE 358
             +      +VKA+S IKNVALINI GA M G  GT AR+F AL    VN+++ISQGSSE
Sbjct: 301 VAEKFQCRHVVKAVSLIKNVALINISGAEMPGTVGTVARLFTALARAGVNIVMISQGSSE 360

Query: 359 TNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAK 418
           +N+S VVSE  V+ ALKAL  EF         N  ++++++ D++VCV++VVGAGM G  
Sbjct: 361 SNLSFVVSESHVESALKALHAEF---------NREIVKEITSDRNVCVVAVVGAGMAGTP 411

Query: 419 GIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKF 467
           G+A ++F A+  S  NI MI+QGSS+ NISFV+ E D    V+ LH++F
Sbjct: 412 GVAKRVFGALGNSMINIIMISQGSSQYNISFVVREGDAFAAVKTLHDEF 460


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: 585
Number of extensions: 22
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: 473
Length of database: 472
Length adjustment: 33
Effective length of query: 440
Effective length of database: 439
Effective search space:   193160
Effective search space used:   193160
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 WP_011020190.1 MA_RS00690 (aspartate kinase, monofunctional class)
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.18744.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-144  467.7   2.7   2.6e-144  467.5   2.7    1.0  1  lcl|NCBI__GCF_000007345.1:WP_011020190.1  MA_RS00690 aspartate kinase, mon


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007345.1:WP_011020190.1  MA_RS00690 aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.5   2.7  2.6e-144  2.6e-144       2     441 ..       1     461 [.       1     462 [. 0.96

  Alignments for each domain:
  == domain 1  score: 467.5 bits;  conditional E-value: 2.6e-144
                                 TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keli 66 
                                               ++iV+KFGGtSvg++++i++va+++k+ +e+gnq vVV SA +gvTd+L+e a+ +s + +    ke+ 
  lcl|NCBI__GCF_000007345.1:WP_011020190.1   1 MKIVMKFGGTSVGDGKKIRHVAQLLKRYHEEGNQIVVVTSALGGVTDRLLENARLASTKGKvslvKEFK 69 
                                               679*****************************************************9999989999999 PP

                                 TIGR00657  67 ekirekhlealeela.sqalkeklkallekeleevkk............ereldlilsvGEklSaalla 122
                                               +++ +kh ea++ ++  + +++++ ++l+ ++ee++k            +r+ d+i s+GE+l+a++++
  lcl|NCBI__GCF_000007345.1:WP_011020190.1  70 TELTNKHHEAVKDAIeDPRVAKEVLQVLDLRIEELEKaligicylgeltSRSIDYISSYGERLAAPIVS 138
                                               99************999999***************99******************************** PP

                                 TIGR00657 123 aaleelgvkavsllgaeagiltdsefgrAk...vleeikterleklleegiivvvaGFiGatekgeitt 188
                                               +a+++lg+ +++++g+eagi+t+s +g+A+   +++e   +rl   le  +i vv+GFiG +e+g itt
  lcl|NCBI__GCF_000007345.1:WP_011020190.1 139 GAVRSLGAASIEYTGGEAGIVTTSDYGNARpleKTYELVLKRLGCRLES-HILVVTGFIGENEDGIITT 206
                                               ******************************7666666666666666665.599**************** PP

                                 TIGR00657 189 LGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtl 257
                                               LGR GSD++A++l+aalkAde++++++V+Gi+t+DPrivpeA+ +++isy+Ea+EL+++Ga vLhprt+
  lcl|NCBI__GCF_000007345.1:WP_011020190.1 207 LGRSGSDFSASILGAALKADEIWLWKEVNGIMTTDPRIVPEAKTIPQISYAEAMELSYFGANVLHPRTI 275
                                               ********************************************************************* PP

                                 TIGR00657 258 epamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfga 324
                                               epamr  ip++vk+tfnpe +GTl+va++  + +  vka+sl kn al+++sg++m   +g++a++f+a
  lcl|NCBI__GCF_000007345.1:WP_011020190.1 276 EPAMREHIPVRVKNTFNPEFPGTLVVAEKF-QCRHVVKAVSLIKNVALINISGAEMPgtVGTVARLFTA 343
                                               ****************************66.6669*********************999********** PP

                                 TIGR00657 325 laeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksap 393
                                               la+a+vn+++i+q sse+++sfvv+++++++a ++l+ ++ + + ++e++ ++++++v++vGagm+++p
  lcl|NCBI__GCF_000007345.1:WP_011020190.1 344 LARAGVNIVMISQGSSESNLSFVVSESHVESALKALH-AEFNREIVKEITSDRNVCVVAVVGAGMAGTP 411
                                               ***********************************96.68899999*********************** PP

                                 TIGR00657 394 gvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441
                                               gva+++f aL ++ ini mis  ss+++is+vv+e da +av++lh++++
  lcl|NCBI__GCF_000007345.1:WP_011020190.1 412 GVAKRVFGALGNSMINIIMISqgSSQYNISFVVREGDAFAAVKTLHDEFE 461
                                               ***********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (472 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: 12.32
//
[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