Alignments for a candidate for asp-kinase in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Shewanella amazonensis SB2B

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate 6936867 Sama_1049 aspartate kinase (RefSeq)

Query= SwissProt::A4VJB4
         (412 letters)



>FitnessBrowser__SB2B:6936867
          Length = 403

 Score =  327 bits (838), Expect = 4e-94
 Identities = 185/402 (46%), Positives = 267/402 (66%), Gaps = 4/402 (0%)

Query: 3   LIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQPV 62
           + V+KFGGTSVGT ERIE VA+ + K    G+  V+V+SAM+GETNRL  +A  I     
Sbjct: 4   IYVKKFGGTSVGTFERIEAVADAIAKAHFEGERQVLVLSAMAGETNRLYAMAANIDPLAP 63

Query: 63  PRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQRIQ 122
            RELD++VS GEQV+IAL+++AL +RGV A S  G+QV++ T+S   +A I  +D   + 
Sbjct: 64  ARELDMLVSAGEQVSIALMSIALARRGVNARSLLGSQVKVRTNSQFGRASIESVDTGLLM 123

Query: 123 RDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182
           + +  G V V+AGFQGV+E+G++TTLGRGGSDTT VA+AAAL+A ECQI+TDV GV+TTD
Sbjct: 124 QLLDEGAVPVIAGFQGVNEQGDVTTLGRGGSDTTAVAIAAALEAAECQIFTDVTGVFTTD 183

Query: 183 PRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLITL 242
           P +   AQ+LD I+FE M EMA  G+KVL   +V  A ++ V LRVL SF+ G GTLI  
Sbjct: 184 PNIDPDAQKLDSISFEAMYEMARQGAKVLHPDSVACARRHGVVLRVLSSFESGSGTLIRF 243

Query: 243 DEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAHDN 302
           DE E     I+ GIA  R +  +++ G+ D P     +   ++ A+V+ D++VQ +A + 
Sbjct: 244 DEPEHSGSGIV-GIAVTRGQGLVSVAGLVDQPQAEVALFQALANASVDTDLVVQ-LAEEK 301

Query: 303 TTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRMFE 362
                FT+ +   +  L ++  +A E    +   ++ +AKVS+V  G    A V +R+ E
Sbjct: 302 A--LAFTLAQGALDKVLTLIDRLALEQPLADVRHESPLAKVSLVSTGKAVMAEVGARVTE 359

Query: 363 ALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404
            L  +NI ++++STSEIK+SVVI+E +L+ AVR+LH AF+L+
Sbjct: 360 LLEAQNIRVKLLSTSEIKLSVVIDEVHLQHAVRSLHRAFDLN 401


Lambda     K      H
   0.317    0.133    0.357 

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: 403
Number of extensions: 17
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: 412
Length of database: 403
Length adjustment: 31
Effective length of query: 381
Effective length of database: 372
Effective search space:   141732
Effective search space used:   141732
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 6936867 Sama_1049 (aspartate kinase (RefSeq))
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.27105.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-118  382.7   5.5   7.6e-103  330.8   2.5    2.0  2  lcl|FitnessBrowser__SB2B:6936867  Sama_1049 aspartate kinase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936867  Sama_1049 aspartate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.1e-18   1.1e-18       3      59 ..       4      60 ..       2      64 .. 0.94
   2 !  330.8   2.5  7.6e-103  7.6e-103     103     440 ..      64     398 ..      56     400 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.1e-18
                         TIGR00657  3 liVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvss 59
                                      + V KFGGtSvg++eri++va+ + k++ +g+  v V+SAmag T++L ++a ++++
  lcl|FitnessBrowser__SB2B:6936867  4 IYVKKFGGTSVGTFERIEAVADAIAKAHFEGERQVLVLSAMAGETNRLYAMAANIDP 60
                                      5699***********************************************998876 PP

  == domain 2  score: 330.8 bits;  conditional E-value: 7.6e-103
                         TIGR00657 103 ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrAkvleeikterleklleegiivvvaGFiG 179
                                        reld+++s GE++S+al++ al ++gv+a+sllg++ +++t+s+fgrA+ +e+++t  l +ll+eg ++v+aGF+G
  lcl|FitnessBrowser__SB2B:6936867  64 ARELDMLVSAGEQVSIALMSIALARRGVNARSLLGSQVKVRTNSQFGRAS-IESVDTGLLMQLLDEGAVPVIAGFQG 139
                                       699***********************************************.************************** PP

                         TIGR00657 180 atekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprt 256
                                       ++e+g++ttLGRGGSD+tA+++Aaal+A e++i+tDV G++t+DP+i p+A++ld+is+e + E+a+ GakvLhp++
  lcl|FitnessBrowser__SB2B:6936867 140 VNEQGDVTTLGRGGSDTTAVAIAAALEAAECQIFTDVTGVFTTDPNIDPDAQKLDSISFEAMYEMARQGAKVLHPDS 216
                                       ***************************************************************************** PP

                         TIGR00657 257 lepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvd 333
                                       +  a+r+++ ++v s+f+    GTli  ++ +++ + + ++++++ q lvsv+g  ++p+    +f+ala+a+v+ d
  lcl|FitnessBrowser__SB2B:6936867 217 VACARRHGVVLRVLSSFESG-SGTLIRFDEPEHSGSGIVGIAVTRGQGLVSVAGLVDQPQAEVALFQALANASVDTD 292
                                       *****************998.********999999****************************************** PP

                         TIGR00657 334 lilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeenini 410
                                       l++q ++e+ ++f++ +  +dk  +l +  +  e+ l +v+ e+ la+vslv+ g +    v a+++e L+ +ni +
  lcl|FitnessBrowser__SB2B:6936867 293 LVVQLAEEKALAFTLAQGALDKVLTLID-RLALEQPLADVRHESPLAKVSLVSTGKAVMAEVGARVTELLEAQNIRV 368
                                       **************************96.5777888899************************************** PP

                         TIGR00657 411 emissseikisvvvdekdaekavealhekl 440
                                       + +s+seik+svv+de   ++av+ lh+++
  lcl|FitnessBrowser__SB2B:6936867 369 KLLSTSEIKLSVVIDEVHLQHAVRSLHRAF 398
                                       ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (403 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 3.11
//
[ok]

This GapMind analysis is from Apr 09 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