GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Lacinutrix algicola AKS293

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_055437364.1 ASC41_RS14495 bifunctional aspartate kinase/homoserine dehydrogenase I

Query= reanno::Cola:Echvi_2000
         (815 letters)



>NCBI__GCF_001418085.1:WP_055437364.1
          Length = 814

 Score =  722 bits (1863), Expect = 0.0
 Identities = 370/814 (45%), Positives = 560/814 (68%), Gaps = 3/814 (0%)

Query: 1   MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60
           M+++KFGG+S+ + +NI KV +I+E  S+K+    V SA GG+T++LL+  N+A+ + ++
Sbjct: 1   MQVLKFGGTSVGSSKNINKVITILEDYSKKDKVICVVSAVGGITDKLLKAGNLAKDNNKN 60

Query: 61  YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120
           Y T  + ++ +H++++++L+P Q  +  +  +  +  +L +L  GI+LI E S +T D +
Sbjct: 61  YKTEYKSIKAKHIKVLEELIP-QNNAAIIKELDGKLKKLKNLLDGIFLINELSPQTSDRL 119

Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHF-KSH 179
           +SFGE LS+FI+A  L+++G+     + + L+ T+  +  A+V F+TTN  IQ++F ++ 
Sbjct: 120 VSFGELLSSFIIAETLKSRGVNAVRKNTQQLIVTNSNYTKAEVIFETTNNNIQEYFNEAT 179

Query: 180 DDIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239
            DI ++ GFI  +  G+TTT+GR GSDYTA+I AAAL  E++EIWTDVSG+ T +P+LV 
Sbjct: 180 QDITLLPGFISKSYLGKTTTLGRGGSDYTAAIVAAALKTERLEIWTDVSGMYTTNPKLVK 239

Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSG- 298
            A+ I ++SY+EAMELSHFGAKV++P T+QP +  +IPI+IKNT KP+E GT IS +   
Sbjct: 240 QAYPIERISYHEAMELSHFGAKVLYPPTVQPVLSLNIPIHIKNTLKPNEFGTIISNEGNT 299

Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358
           +     GI+++++I++L +QG G+V + G S+R F TL+   INIILI+QASSEHSIC  
Sbjct: 300 KSSTATGITNINDIALLTLQGNGMVGIPGFSKRLFETLSQEKINIILITQASSEHSICFG 359

Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418
           I+  DA +A++ I   F +EI    +D I +  ++++IA+VG+NM+ + G SG+MF ALG
Sbjct: 360 ISKDDAIQAETAINLAFEHEISKHRIDPITVEQNLSIIALVGDNMKSHQGISGKMFSALG 419

Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKAL 478
           +NN+N+ AIAQG+SE NISAVI + D++KALN +HE FF ++ K L++F+ G+G +G+ L
Sbjct: 420 KNNINIRAIAQGASERNISAVIAEKDVEKALNTIHERFFGNNIKQLNVFITGIGNVGEKL 479

Query: 479 TKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIGT 538
              IHQQ   L++   LD++I GMANS+ M F+ +G DL        + +   +D F+  
Sbjct: 480 IDQIHQQSNYLKKNLKLDVRIVGMANSKKMIFNAEGIDLNDWASKFHHADKSTLDGFLEK 539

Query: 539 MTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQRG 598
              +N  NS+FVD TA+  V+ +YE  L S + +V  NK A S     YK L+ LA +  
Sbjct: 540 AKALNLRNSIFVDITANDAVSKMYEHYLRSSIAVVACNKIACSSTYSNYKLLQDLALKYN 599

Query: 599 VRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQA 658
             FFYETNV AGLP+INTL +L+ SGD V  I+AVLSGS+N++F+       F + V +A
Sbjct: 600 TPFFYETNVGAGLPIINTLNNLVSSGDKVTSIQAVLSGSLNFVFNNFSDKTNFHDTVKRA 659

Query: 659 KEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFFK 718
           + +GYTEPDPR DLSG+DVARKILIL RE G  +  E +E  S + +   ++ +V +F+K
Sbjct: 660 QFEGYTEPDPRIDLSGIDVARKILILARENGGAMEIESIENDSFLTKANLESDTVDDFYK 719

Query: 719 KLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILFT 778
            L+  + HFQ+L   A AK  +L+++A  +NGKAKVGL  +   HPF+ L+G DN+++F 
Sbjct: 720 TLKTEEAHFQKLYASAKAKNCQLKYVAEFKNGKAKVGLKEIPEGHPFYNLEGKDNIVMFY 779

Query: 779 TERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812
           TERY + P+IV+G GAGADVTA+G+FADII+ G+
Sbjct: 780 TERYPEQPLIVKGAGAGADVTASGLFADIIKAGS 813


Lambda     K      H
   0.317    0.134    0.375 

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: 1557
Number of extensions: 76
Number of successful extensions: 6
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: 815
Length of database: 814
Length adjustment: 41
Effective length of query: 774
Effective length of database: 773
Effective search space:   598302
Effective search space used:   598302
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 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate WP_055437364.1 ASC41_RS14495 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.1078584.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-126  409.1   6.3   1.7e-126  408.8   6.3    1.1  1  NCBI__GCF_001418085.1:WP_055437364.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055437364.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.8   6.3  1.7e-126  1.7e-126       5     441 ..       3     458 ..       1     459 [. 0.95

  Alignments for each domain:
  == domain 1  score: 408.8 bits;  conditional E-value: 1.7e-126
                             TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 
                                           V+KFGGtSvg+ ++i+kv  i++  ++k+ +v+ VvSA++g+Td+L++  + ++++++  k++ + i++kh++
  NCBI__GCF_001418085.1:WP_055437364.1   3 VLKFGGTSVGSSKNINKVITILEDYSKKD-KVICVVSAVGGITDKLLKAGNLAKDNNKnyKTEYKSIKAKHIK 74 
                                           99*****************9998888666.***************************9999999********* PP

                             TIGR00657  76 aleelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsll 136
                                            leel++q+ ++ + + l+ +l+++k+            +++ d+++s+GE lS+ ++a++l+++gv+av   
  NCBI__GCF_001418085.1:WP_055437364.1  75 VLEELIPQNNAA-IIKELDGKLKKLKNlldgiflinelsPQTSDRLVSFGELLSSFIIAETLKSRGVNAVR-K 145
                                           ******865555.555556666666667999***********************************76665.6 PP

                             TIGR00657 137 gaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207
                                           + ++ i+t+s++++A+v+ e+++++++++ +e    i ++ GFi  +  g++ttLGRGGSD+tAa++Aaalk 
  NCBI__GCF_001418085.1:WP_055437364.1 146 NTQQLIVTNSNYTKAEVIFETTNNNIQEYFNEAtqDITLLPGFISKSYLGKTTTLGRGGSDYTAAIVAAALKT 218
                                           88999************************9999889************************************* PP

                             TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGT 280
                                           +++ei+tDV+G yt+ P++v++A  ++ isy+Ea+EL+++GakvL+p t++p+  ++ipi++k+t  p++ GT
  NCBI__GCF_001418085.1:WP_055437364.1 219 ERLEIWTDVSGMYTTNPKLVKQAYPIERISYHEAMELSHFGAKVLYPPTVQPVLSLNIPIHIKNTLKPNEFGT 291
                                           ************************************************************************* PP

                             TIGR00657 281 livakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdke 351
                                           +i ++ + ++++  +++++ ++ al++++g++m   pg+ +++f++l+++k+n++li+q sse+si f ++k+
  NCBI__GCF_001418085.1:WP_055437364.1 292 IISNEGN-TKSSTATGITNINDIALLTLQGNGMVgiPGFSKRLFETLSQEKINIILITQASSEHSICFGISKD 363
                                           *****98.5559************************************************************* PP

                             TIGR00657 352 dadkakellk...kkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseik 419
                                           da +a+++ +   +++ +++ + +++ve++l++++lvG++mks+ g+ +k+f+aL ++nini++i+  +se++
  NCBI__GCF_001418085.1:WP_055437364.1 364 DAIQAETAINlafEHEISKHRIDPITVEQNLSIIALVGDNMKSHQGISGKMFSALGKNNINIRAIAqgASERN 436
                                           *999999988888889999***********************************************9****** PP

                             TIGR00657 420 isvvvdekdaekavealheklv 441
                                           is v+ ekd+eka++++he+++
  NCBI__GCF_001418085.1:WP_055437364.1 437 ISAVIAEKDVEKALNTIHERFF 458
                                           *******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (814 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: 48.42
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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