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

GapMind for Amino acid biosynthesis

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

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_055436340.1 ASC41_RS09190 aspartate kinase

Query= BRENDA::P08660
         (449 letters)



>NCBI__GCF_001418085.1:WP_055436340.1
          Length = 442

 Score =  239 bits (610), Expect = 1e-67
 Identities = 151/453 (33%), Positives = 247/453 (54%), Gaps = 24/453 (5%)

Query: 4   IVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERFEK 63
           ++V KFGGTSV   + M    +I+ +D   ++VVLSA +G TN LV ++E ++ G   E 
Sbjct: 1   MLVLKFGGTSVGSIENMINVKNII-NDGEKKVVVLSAMSGTTNALVKISEYIKNGNVDEA 59

Query: 64  L---DAIR-NIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGE 119
           L   DA+R N    I   +   ++ +     + +    L           L +++V+ GE
Sbjct: 60  LIVIDALRTNYNSTIKTFIINKDLYKTAFVYVNDVFNTLEALVNKRFDTLLYNQIVAQGE 119

Query: 120 LMSTLLFVEILRERDVQAQWF---DVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNE 176
           L+ST +F   L +  + A      D  ++ +TN      EPD   + +     +    + 
Sbjct: 120 LLSTFIFTHYLLQEGINASLLPALDFMRIDKTN------EPDNYYIQQNLNRIMAETPDS 173

Query: 177 GLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSA 236
            + ITQGFI  + +G    L RGGSDYTA ++   L A  V IWTD+ G +  DPR V  
Sbjct: 174 EIYITQGFISRDAEGNIANLQRGGSDYTATIIGAVLKAEEVQIWTDIDGFHNNDPRFVEN 233

Query: 237 AKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENP 296
              I  ++F E+AE+A FGAK+LHP T++P    DIPV + ++ DP A GTL+ N+    
Sbjct: 234 TTAISNLSFDESAELAYFGAKILHPQTVMPVSVFDIPVRLKNTMDPEAHGTLITNQVHGE 293

Query: 297 PLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTT 356
            + +A+A +   T + + S+ ML + GFL +VF I  R+  ++D+ITTSE++V+LT+D  
Sbjct: 294 GI-KAIAAKDGITAIKIKSVRMLLAHGFLKKVFEIFERYETAIDMITTSEIAVSLTID-- 350

Query: 357 GSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIR 416
                 DT   ++++ EL+    VEV++ +++V L+GN++         +F +L+  ++R
Sbjct: 351 ------DTRHLEAIVNELNKFAVVEVDDYMSIVCLVGNEIIFHTDT-PNLFQILQDVSVR 403

Query: 417 MICYGASSHNLCFLVPGEDAEQVVQKLHSNLFE 449
           MI YG S++N+  L+   D  + +QKL   +FE
Sbjct: 404 MISYGGSNNNISLLINTSDKIETLQKLQRYVFE 436


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: 380
Number of extensions: 18
Number of successful extensions: 7
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: 442
Length adjustment: 32
Effective length of query: 417
Effective length of database: 410
Effective search space:   170970
Effective search space used:   170970
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_055436340.1 ASC41_RS09190 (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.1072012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.2e-89  287.4   4.1    1.3e-89  287.2   4.1    1.0  1  NCBI__GCF_001418085.1:WP_055436340.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055436340.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.2   4.1   1.3e-89   1.3e-89       4     441 ..       2     435 ..       1     436 [. 0.90

  Alignments for each domain:
  == domain 1  score: 287.2 bits;  conditional E-value: 1.3e-89
                             TIGR00657   4 iVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee...keliekirekh 73 
                                           +V+KFGGtSvg++e++ +v +i+   +    + vVV+SAm+g+T+aLv+++e +++++      +i+++r++ 
  NCBI__GCF_001418085.1:WP_055436340.1   2 LVLKFGGTSVGSIENMINVKNIINDGE----KKVVVLSAMSGTTNALVKISEYIKNGNVdeaLIVIDALRTNY 70 
                                           69*****************99998766....779***********************9965545677778888 PP

                             TIGR00657  74 lealeela.sqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgvkavsllga 138
                                            +++++++ ++ l ++    ++  ++ +++          +  i++ GE lS+ +++ +l ++g  ++sll a
  NCBI__GCF_001418085.1:WP_055436340.1  71 NSTIKTFIiNKDLYKTAFVYVNDVFNTLEAlvnkrfdTLLYNQIVAQGELLSTFIFTHYLLQEG-INASLLPA 142
                                           8889999988877777777777777777778877888888999*********************.67788888 PP

                             TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeve 211
                                              ++ d++ +  ++ ++ + +r+ +      i++++GFi  + +g+i  L RGGSD+tA++++a lkA+ev+
  NCBI__GCF_001418085.1:WP_055436340.1 143 LDFMRIDKTNEPDNYYIQQNLNRIMAETPDSEIYITQGFISRDAEGNIANLQRGGSDYTATIIGAVLKAEEVQ 215
                                           88888888888878788888888888888889***************************************** PP

                             TIGR00657 212 iytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTliva 284
                                           i+tD+dG +  DPr v+++  + ++s++E +ELa++Gak+Lhp+t+ p+  ++ip++ k+t++pea GTli++
  NCBI__GCF_001418085.1:WP_055436340.1 216 IWTDIDGFHNNDPRFVENTTAISNLSFDESAELAYFGAKILHPQTVMPVSVFDIPVRLKNTMDPEAHGTLITN 288
                                           ************************************************************************* PP

                             TIGR00657 285 kskseeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadk 355
                                           + +    + +ka++ ++  + ++++++ m    g+l++vf++ ++ +  +d+i+  +se  +s+++d++   +
  NCBI__GCF_001418085.1:WP_055436340.1 289 QVH---GEGIKAIAAKDGITAIKIKSVRMLlaHGFLKKVFEIFERYETAIDMIT--TSEIAVSLTIDDTR--H 354
                                           *55...578********************999**********************..77767777777655..4 PP

                             TIGR00657 356 akellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvde 426
                                            +++    v+e++++  vev++ +++v lvG++++ +   + ++f+ L++  ++++mis   s+ +is++++ 
  NCBI__GCF_001418085.1:WP_055436340.1 355 LEAI----VNELNKFAVVEVDDYMSIVCLVGNEIIFHT-DTPNLFQILQD--VSVRMISygGSNNNISLLINT 420
                                           4444....346789999******************955.5789*****99..*******999*********** PP

                             TIGR00657 427 kdaekavealheklv 441
                                           +d ++++++l++ ++
  NCBI__GCF_001418085.1:WP_055436340.1 421 SDKIETLQKLQRYVF 435
                                           *********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (442 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: 16.93
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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