Alignments for a candidate for asp-kinase in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Halomonas desiderata SP1

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_086511746.1 BZY95_RS20540 hypothetical protein

Query= BRENDA::Q5JK18
         (570 letters)



>NCBI__GCF_002151265.1:WP_086511746.1
          Length = 450

 Score =  145 bits (367), Expect = 3e-39
 Identities = 105/327 (32%), Positives = 163/327 (49%), Gaps = 17/327 (5%)

Query: 94  GGDQLSVVMKFGGSSVSSAARMREVAGLILAFPEERPVVVLSAMGKTTNLLLLAGEKAVG 153
           G   ++ V KFGG+S+  A  +R +  L+    +   VVV+SAMGKTTN L      A G
Sbjct: 13  GEPDMTTVFKFGGASIKDADAIRHLTPLLERHRDRPLVVVVSAMGKTTNKLEALLAAARG 72

Query: 154 CGVIRVSEIEE-WNLIKDLHIKTVEELA-----LPRSVIHTMLDELEQLLKGIAMMKELT 207
            G  +  E    +  ++  H + +E L       PR  +  + DEL+   +         
Sbjct: 73  EGGTQGDEYRRCFEALQTEHREAIEALFGDAADSPRECVDALFDELDAQHRRHRDSDHA- 131

Query: 208 LRTTDYLVSFGECMSTRIFAAYLNKIGVKARQYDAFDIGFITTDDFGNADILE--ATYPA 265
            +  D  V +GE +ST I AA+LN   +    +DA ++  + TD    A  L+   T   
Sbjct: 132 -KHYDQTVCYGELISTTIVAAWLNHNDIATDWHDAREL--VRTDACYQAANLDWSTTAET 188

Query: 266 VAKRLHGDWIRDPAIPIVTGFLGKGWKSGAVTTLGRGGSDLTATTIGKALGLREIQVWKD 325
           V +RL G       + +  GF+G G   G  TTLGR GSD +A      L  RE+ +WKD
Sbjct: 189 VRQRLAGS----DRVILTQGFIG-GTAEGEATTLGREGSDFSAAIFAHCLDAREVVIWKD 243

Query: 326 VDGVLTCDPNIYPNATTVPYLTFEEAAELAYFGAQVLHPQSMRPAREGDIPVRVKNSYNP 385
           V G+   DP  + NA  +  +++ EA E A+ GA+V+HP+++ P +E  IP+ V++   P
Sbjct: 244 VTGLFNADPRRFDNAVQLERISYAEATERAWHGAKVIHPKTLGPLQEKSIPLTVRSFETP 303

Query: 386 KAPGTLITKQREMDKVVLTSIVLKSNV 412
            A  T+I  +R  D  V + I+ ++ V
Sbjct: 304 DAEPTVIDAERRFDSDVASCILREAQV 330


Lambda     K      H
   0.320    0.136    0.388 

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: 424
Number of extensions: 24
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: 570
Length of database: 450
Length adjustment: 34
Effective length of query: 536
Effective length of database: 416
Effective search space:   222976
Effective search space used:   222976
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: 52 (24.6 bits)

Align candidate WP_086511746.1 BZY95_RS20540 (hypothetical protein)
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.26449.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-73  233.7   0.0    2.6e-73  233.5   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511746.1  BZY95_RS20540 hypothetical prote


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511746.1  BZY95_RS20540 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.5   0.0   2.6e-73   2.6e-73       2     330 ..      17     359 ..      16     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 233.5 bits;  conditional E-value: 2.6e-73
                                 TIGR00657   2 aliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee......ke 64 
                                               ++ V KFGG S+++++ i+++  ++++++  +++ vVVvSAm+++T++L +l   +  e         +
  lcl|NCBI__GCF_002151265.1:WP_086511746.1  17 MTTVFKFGGASIKDADAIRHLTPLLERHR--DRPLVVVVSAMGKTTNKLEALLAAARGEGGtqgdeyRR 83 
                                               678*********************99988..789******************99998877778888877 PP

                                 TIGR00657  65 liekirekhlealeela...sqalkeklkallekeleevkk......ereldlilsvGEklSaallaaa 124
                                                 e+++++h ea+e+l     ++ +e + al ++  ++ ++       +++d  +++GE +S++++aa+
  lcl|NCBI__GCF_002151265.1:WP_086511746.1  84 CFEALQTEHREAIEALFgdaADSPRECVDALFDELDAQHRRhrdsdhAKHYDQTVCYGELISTTIVAAW 152
                                               7888888888888887542234456666666666666655599999999******************** PP

                                 TIGR00657 125 leelgvkavsllgaeagiltdsefgrAkvleeikterleklleeg.iivvvaGFiGatekgeittLGRG 192
                                               l++ +  a ++ +a++ ++td+ ++ A+   ++++e + + l     + +++GFiG t +ge ttLGR 
  lcl|NCBI__GCF_002151265.1:WP_086511746.1 153 LNHND-IATDWHDARELVRTDACYQAANLDWSTTAETVRQRLAGSdRVILTQGFIGGTAEGEATTLGRE 220
                                               *****.99********************777888888888877767*********************** PP

                                 TIGR00657 193 GSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepam 261
                                               GSD++Aa+ A++l+A+ev i++DV G + aDPr   +A +l+ isy+Ea E a +Gakv+hp+tl p+ 
  lcl|NCBI__GCF_002151265.1:WP_086511746.1 221 GSDFSAAIFAHCLDAREVVIWKDVTGLFNADPRRFDNAVQLERISYAEATERAWHGAKVIHPKTLGPLQ 289
                                               ********************************************************************* PP

                                 TIGR00657 262 rakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk...pgilaevfgalae 327
                                               +++ip+ v+s   p+ae T+i a++    ++ v +  l++ q+ v+v+             +++g+l +
  lcl|NCBI__GCF_002151265.1:WP_086511746.1 290 EKSIPLTVRSFETPDAEPTVIDAERRF--DSDVASCILREAQVWVEVRPRDFSfmdEPRQHDILGRLVK 356
                                               ************************773..3578888888888888887665554445555566666655 PP

                                 TIGR00657 328 akv 330
                                               a+ 
  lcl|NCBI__GCF_002151265.1:WP_086511746.1 357 AGL 359
                                               555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (450 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.39
//
[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