Alignments for a candidate for asp-kinase in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Methanobacterium lacus AL-21

Align Aspartokinase; EC 2.7.2.4; Aspartate kinase (uncharacterized)
to candidate WP_013645478.1 METBO_RS09425 aspartate kinase

Query= curated2:Q59229
         (411 letters)



>NCBI__GCF_000191585.1:WP_013645478.1
          Length = 406

 Score =  169 bits (427), Expect = 2e-46
 Identities = 138/414 (33%), Positives = 207/414 (50%), Gaps = 21/414 (5%)

Query: 1   MGLIVQKFGGTSVGSVERILNVANRVIEEKKNGNDVVVVVSAMGKTTDELVDLAKQISAH 60
           M +IV KFGGTS+G+ +RI   A  V++E   G  VVVVVSA+ KTTD+++         
Sbjct: 1   MEIIVAKFGGTSIGNGDRIRKAAESVVKEYMKGKKVVVVVSAINKTTDDILKTVDDAIGE 60

Query: 61  P--PKREMDMLLTTGEQVTISLLAMALNEKG----YEAISYTGWQAGITTEPVFGNARIL 114
              PK+  D +++ GE  ++ + +  +   G    Y      GW   I T+  + NA + 
Sbjct: 61  SITPKQLAD-IVSMGEITSVRIFSSTIESLGVKSEYIDPRAEGWP--IITDSDYLNADVN 117

Query: 115 NIETEK----IQKQLNEGKIVVVAGFQGIDEHGEITTLGRGGSDTTAVALAAALKAEKCD 170
              TEK    + K L++G I V+ GF G DE G ITTLGRGGSD TA  L   LKAE+  
Sbjct: 118 FELTEKKCEELIKILDQGIIPVLCGFVGRDEDGTITTLGRGGSDITAFLLGHCLKAEEVV 177

Query: 171 IYTDVTGVFTTDPRYVKSARKLASISYDEMLELANLGAGVLHPRAVEFAKNYGITLEVRS 230
           I TDV GV +TDP  ++SA+KL  IS +EM +LA  GA VLHP A+++ K+  I  ++  
Sbjct: 178 IVTDVGGVMSTDPNRLQSAKKLDKISVEEMRDLATHGAKVLHPHALKY-KDPLINAKIIG 236

Query: 231 SMEREEGTIIEEEVTMEQNLVVRGVAFEDE-ITRVTVFG--LPNSLTSLSTIFTTLAQNR 287
               +      E +    N +++  A   E I+ + V G  +      LS +   LAQN 
Sbjct: 237 FEHGDLSAAGTEIIGPAGNHMLKTTALNVEPISVIAVVGEEILTKTGVLSELTDALAQNS 296

Query: 288 INVDIIIQSATDAETTNLSFSIKSDDLEETMAVLENNKNLLNYQGIESETGLAKVSIVGS 347
           IN+   I +  ++ T  +  SI          V+  N++L     I   T +A +++   
Sbjct: 297 INI-YGISTGQNSVTLFIDKSIVDRAHNILHEVVVENQDL---SSISVGTDIAMITVTSQ 352

Query: 348 GMISNPGVAAKMFEVLALNGIQVKMVSTSEIKVSTVVEESQMIKAVEALHQAFE 401
             I  PG+  ++ E L    I +  +S+S+  V   VE     +A E +    E
Sbjct: 353 DFIDTPGIITRITEPLRKKKINIVEISSSQTSVVVFVEWKDGKRAYELVRSVLE 406


Lambda     K      H
   0.313    0.129    0.340 

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: 348
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: 411
Length of database: 406
Length adjustment: 31
Effective length of query: 380
Effective length of database: 375
Effective search space:   142500
Effective search space used:   142500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_013645478.1 METBO_RS09425 (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.32409.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-140  452.1  12.4     1e-139  452.0  12.4    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013645478.1  METBO_RS09425 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013645478.1  METBO_RS09425 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.0  12.4    1e-139    1e-139       1     404 [.       1     405 [.       1     406 [] 0.98

  Alignments for each domain:
  == domain 1  score: 452.0 bits;  conditional E-value: 1e-139
                                 TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 
                                               +e+iV+KFGGts+g+++ri+kaa++v+ke+++gkkvvVVvSA++k+td ++++++     +ai + i+p
  lcl|NCBI__GCF_000191585.1:WP_013645478.1   1 MEIIVAKFGGTSIGNGDRIRKAAESVVKEYMKGKKVVVVVSAINKTTDDILKTVD-----DAIGESITP 64 
                                               79****************************************************8.....********* PP

                                 TIGR00656  70 rerdelvsvGEllssallssalrelgvkaeald..gkeagilTddefgnAkikelate...erLlelLe 133
                                               ++ + +vs+GE +s++++ss ++ lgvk+e++d   + ++i+Td+ + nA ++++ te   e+L+++L+
  lcl|NCBI__GCF_000191585.1:WP_013645478.1  65 KQLADIVSMGEITSVRIFSSTIESLGVKSEYIDprAEGWPIITDSDYLNADVNFELTEkkcEELIKILD 133
                                               *********************************877889****************999999******** PP

                                 TIGR00656 134 egiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidki 202
                                               +gii+v +GF+G++e+G iTtLGRGGSD+tA+ll+++lkA++v+i+TDV Gv++tDP+ +++akk+dki
  lcl|NCBI__GCF_000191585.1:WP_013645478.1 134 QGIIPVLCGFVGRDEDGTITTLGRGGSDITAFLLGHCLKAEEVVIVTDVGGVMSTDPNRLQSAKKLDKI 202
                                               ********************************************************************* PP

                                 TIGR00656 203 syeEalelAtlGakvlhpralela.veakvpilvrsskeke.egTlitnkkensslvkaialekn.var 268
                                               s+eE+++lAt+Gakvlhp+al+++   ++++i+++++ + + +gT+i+    n+ ++k++al+ + +++
  lcl|NCBI__GCF_000191585.1:WP_013645478.1 203 SVEEMRDLATHGAKVLHPHALKYKdPLINAKIIGFEHGDLSaAGTEIIGPAGNH-MLKTTALNVEpISV 270
                                               ************************8899*************9***********9.********999*** PP

                                 TIGR00656 269 ltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaae.les 336
                                               ++v+ge++l k+g+l+e++ aLa+++in+  is+++  +s++l++d+  vd+a+++L+e++ + + l+s
  lcl|NCBI__GCF_000191585.1:WP_013645478.1 271 IAVVGEEILTKTGVLSELTDALAQNSINIYGISTGQ--NSVTLFIDKSIVDRAHNILHEVVVENQdLSS 337
                                               ************************************..*********************9987767*** PP

                                 TIGR00656 337 leveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404
                                               ++v  d+a++++ +++++++pG++++i+++l++k+ini++isss+t+++v+v++kd ++a+++++++l
  lcl|NCBI__GCF_000191585.1:WP_013645478.1 338 ISVGTDIAMITVTSQDFIDTPGIITRITEPLRKKKINIVEISSSQTSVVVFVEWKDGKRAYELVRSVL 405
                                               ****************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (406 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.33
//
[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