Alignments for a candidate for asp-kinase in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Klebsiella variicola At-22

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_008807318.1 KVAR_RS24120 lysine-sensitive aspartokinase 3

Query= BRENDA::P08660
         (449 letters)



>NCBI__GCF_000025465.1:WP_008807318.1
          Length = 449

 Score =  764 bits (1972), Expect = 0.0
 Identities = 393/449 (87%), Positives = 417/449 (92%)

Query: 1   MSEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGER 60
           M+++VV+KFGGTSVADFDAMNRS D+ L DAN R+VVLSASAG+TN+LVALA GLEP ER
Sbjct: 1   MTDLVVAKFGGTSVADFDAMNRSIDVALLDANTRIVVLSASAGVTNILVALAGGLEPTER 60

Query: 61  FEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGEL 120
           F +LDA+R IQF ILERLRYPNVIREEIERLLENIT LAEAAALA+S ALTDELVSHGEL
Sbjct: 61  FSQLDALRQIQFNILERLRYPNVIREEIERLLENITTLAEAAALASSTALTDELVSHGEL 120

Query: 121 MSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVI 180
           MSTLLFVEILRER +QAQWFD RKV+RTNDRFGRAEPDIAA+AEL   QL PRL EGLV+
Sbjct: 121 MSTLLFVEILRERGIQAQWFDARKVLRTNDRFGRAEPDIAAVAELTQQQLAPRLAEGLVV 180

Query: 181 TQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRI 240
           TQGFIGSE KGRTTTLGRGGSDYTAALL EAL+A+RVDIWTDVPGIYTTDPRV  AAKRI
Sbjct: 181 TQGFIGSEAKGRTTTLGRGGSDYTAALLGEALNATRVDIWTDVPGIYTTDPRVAPAAKRI 240

Query: 241 DEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFR 300
           D IAF EAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSK+P+AGGTLVC  TENPPLFR
Sbjct: 241 DVIAFEEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKEPKAGGTLVCKTTENPPLFR 300

Query: 301 ALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTS 360
           ALALRR QTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALT+DTTGSTS
Sbjct: 301 ALALRRRQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTMDTTGSTS 360

Query: 361 TGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICY 420
            GDTLLTQ+LL ELS+LCRVEVEE LALVALIGN+LSKACGVGKEVFGVLEPFNIRMICY
Sbjct: 361 AGDTLLTQALLTELSSLCRVEVEEDLALVALIGNELSKACGVGKEVFGVLEPFNIRMICY 420

Query: 421 GASSHNLCFLVPGEDAEQVVQKLHSNLFE 449
           GASSHNLCFLVPG DAE+VVQKLH NLFE
Sbjct: 421 GASSHNLCFLVPGADAEKVVQKLHHNLFE 449


Lambda     K      H
   0.320    0.135    0.376 

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: 634
Number of extensions: 15
Number of successful extensions: 1
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: 449
Length of database: 449
Length adjustment: 33
Effective length of query: 416
Effective length of database: 416
Effective search space:   173056
Effective search space used:   173056
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: 51 (24.3 bits)

Align candidate WP_008807318.1 KVAR_RS24120 (lysine-sensitive aspartokinase 3)
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.1881675.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-149  481.9   0.2   9.9e-149  481.7   0.2    1.0  1  NCBI__GCF_000025465.1:WP_008807318.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_008807318.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.7   0.2  9.9e-149  9.9e-149       2     406 ..       3     449 .]       2     449 .] 0.96

  Alignments for each domain:
  == domain 1  score: 481.7 bits;  conditional E-value: 9.9e-149
                             TIGR00656   2 eliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelae.............llkll. 60 
                                           +l+V+KFGGtsv+++++++++ + +l +   ++ ++VV+SA+++vt+ lv+la              l++++ 
  NCBI__GCF_000025465.1:WP_008807318.1   3 DLVVAKFGGTSVADFDAMNRSIDVALLD---ANTRIVVLSASAGVTNILVALAGglepterfsqldaLRQIQf 72 
                                           79********************999988...99********************99999999999998444445 PP

                             TIGR00656  61 .........eaisdei..................sprerdelvsvGEllssallssalrelgvkaealdgkea 106
                                                    ++i++ei                  s + +delvs+GEl+s+ l++++lre+g +a+++d +++
  NCBI__GCF_000025465.1:WP_008807318.1  73 nilerlrypNVIREEIerllenittlaeaaalasSTALTDELVSHGELMSTLLFVEILRERGIQAQWFD-ARK 144
                                           5556667777777777888888888888888888***********************************.9** PP

                             TIGR00656 107 gilTddefgnAkikelate....erLlelLeegiivvvaGFiGateeGeiTtLGRGGSDltAallaaalkAdr 175
                                           +++T+d+fg+A+++++a++    ++L+++L+eg +vv++GFiG++ +G++TtLGRGGSD+tAall++al+A r
  NCBI__GCF_000025465.1:WP_008807318.1 145 VLRTNDRFGRAEPDIAAVAeltqQQLAPRLAEG-LVVTQGFIGSEAKGRTTTLGRGGSDYTAALLGEALNATR 216
                                           *****************9999999*********.9************************************** PP

                             TIGR00656 176 veiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrsskeke.egTli 247
                                           v+i+TDV+G+yttDPrv ++ak+id i++eEa+e+At+Gakvlhp++l +av++++p++v sske++  gTl+
  NCBI__GCF_000025465.1:WP_008807318.1 217 VDIWTDVPGIYTTDPRVAPAAKRIDVIAFEEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKEPKaGGTLV 289
                                           *******************************************************************99**** PP

                             TIGR00656 248 tnkkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtesetsislvvdeedvde 320
                                           ++++en++l++a+al++ +++lt+++ +ml++rg+lae+f++La+++i+vdli+++e  +s++l++d++++++
  NCBI__GCF_000025465.1:WP_008807318.1 290 CKTTENPPLFRALALRRRQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSE--VSVALTMDTTGSTS 360
                                           ******************************************************999..************** PP

                             TIGR00656 321 akkaLkeesgaae...lesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvde 390
                                           a ++L ++ +++e   l+++eveedla+v+++g++l++a+Gv +e+f +le++ni+++++++s++++++lv++
  NCBI__GCF_000025465.1:WP_008807318.1 361 AGDTLLTQALLTElssLCRVEVEEDLALVALIGNELSKACGVGKEVFGVLEPFNIRMICYGASSHNLCFLVPG 433
                                           *********99999999******************************************************** PP

                             TIGR00656 391 kdaekavrklheklee 406
                                           +daek+v+klh++l+e
  NCBI__GCF_000025465.1:WP_008807318.1 434 ADAEKVVQKLHHNLFE 449
                                           ************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (449 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: 16.42
//
[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