Alignments for a candidate for asp-kinase in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Caulobacter crescentus NA1000

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate CCNA_00886 CCNA_00886 aspartokinase

Query= SwissProt::A4VJB4
         (412 letters)



>FitnessBrowser__Caulo:CCNA_00886
          Length = 415

 Score =  392 bits (1008), Expect = e-114
 Identities = 221/415 (53%), Positives = 287/415 (69%), Gaps = 13/415 (3%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           M+ +V KFGGTSV  +ERI +VA  V      G  + VVVSAMSG+TN L+         
Sbjct: 1   MSRLVMKFGGTSVADLERIRRVARLVAAEVATGKQVAVVVSAMSGKTNELVAWTDGAGRA 60

Query: 61  PV-----PRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQ 115
                    E D +V++GEQVT  LLAM L   G  A S+ G QV ILTD AH +ARI +
Sbjct: 61  AAGLPESDDEYDAVVASGEQVTAGLLAMTLRNMGHKARSFLGWQVPILTDEAHGRARIEE 120

Query: 116 IDAQRIQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDV 175
           I  + ++     G + V+AGFQGV     ITTLGRGGSDT+ VA+AAA+K D C IYTDV
Sbjct: 121 IPPENLEECFANGEIAVIAGFQGVTPNRRITTLGRGGSDTSAVAIAAAVKGD-CDIYTDV 179

Query: 176 DGVYTTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQE- 234
           DGVYTTDPR+ +KA+RL KI++EEMLEMASLG+KVLQ R+VE A  + VP+RVL SF E 
Sbjct: 180 DGVYTTDPRIESKARRLAKISYEEMLEMASLGAKVLQTRSVEMAMAHRVPVRVLSSFVEP 239

Query: 235 ----GPGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVE 290
               G GT++  DEEE ME+ I+SG+A++RDEAK+T+ G+PD PGV+ +I G ++ ANV 
Sbjct: 240 GEAPGQGTIVC-DEEEIMEKRIVSGVAYSRDEAKITLLGLPDHPGVSSQIFGRLAEANVN 298

Query: 291 VDMIVQNVAHD-NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVG 349
           VDMIVQ+ A   +T +  FTV + D   A++++Q    E+G      + ++AKVS++GVG
Sbjct: 299 VDMIVQSRARSADTANMEFTVGKRDATRAVEIVQAAQKEIGFEAVAVNEDVAKVSVIGVG 358

Query: 350 MRSHAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404
           MRSHAGVA  MF+ALA++NINIQ+ISTSEIK+SV+I+  Y ELAVRALH  + LD
Sbjct: 359 MRSHAGVAQSMFQALAEKNINIQVISTSEIKISVLIDAAYTELAVRALHAVYGLD 413


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: 445
Number of extensions: 22
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: 412
Length of database: 415
Length adjustment: 31
Effective length of query: 381
Effective length of database: 384
Effective search space:   146304
Effective search space used:   146304
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 CCNA_00886 CCNA_00886 (aspartokinase)
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.3038730.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.6e-132  426.5  10.4   6.3e-132  426.3  10.4    1.0  1  FitnessBrowser__Caulo:CCNA_00886  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_00886  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.3  10.4  6.3e-132  6.3e-132       4     405 ..       4     411 ..       1     413 [. 0.94

  Alignments for each domain:
  == domain 1  score: 426.3 bits;  conditional E-value: 6.3e-132
                         TIGR00656   4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdei....sprerdelv 76 
                                        V+KFGGtsv++ eri+++a++v +e+  gk+v VVvSAms++t+elv+ ++      a + +     s+ e d +v
  FitnessBrowser__Caulo:CCNA_00886   4 LVMKFGGTSVADLERIRRVARLVAAEVATGKQVAVVVSAMSGKTNELVAWTDG-----AGRAAAglpeSDDEYDAVV 75 
                                       69*************************************************82.....2222223334899****** PP

                         TIGR00656  77 svGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeGeiT 153
                                       + GE++++ ll++ lr+ g+ka+++ g++ +ilTd+ +g+A+i+e+ + e+L+e  ++g i v+aGF+G t + +iT
  FitnessBrowser__Caulo:CCNA_00886  76 ASGEQVTAGLLAMTLRNMGHKARSFLGWQVPILTDEAHGRARIEEIPP-ENLEECFANGEIAVIAGFQGVTPNRRIT 151
                                       ************************************************.**************************** PP

                         TIGR00656 154 tLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveak 230
                                       tLGRGGSD++A+++aaa+k d ++iyTDV+GvyttDPr+ ++a++++kisyeE+le+A+lGakvl+ r++e+a++  
  FitnessBrowser__Caulo:CCNA_00886 152 TLGRGGSDTSAVAIAAAVKGD-CDIYTDVDGVYTTDPRIESKARRLAKISYEEMLEMASLGAKVLQTRSVEMAMAHR 227
                                       *******************76.9****************************************************** PP

                         TIGR00656 231 vpilvrssk.....ekeegTlitnkkens..slvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdli 300
                                       vp++v ss+      + +gT +++++e    ++v+++a++++ a++t+   g+ +++g+ ++if++Lae+++nvd+i
  FitnessBrowser__Caulo:CCNA_00886 228 VPVRVLSSFvepgeAPGQGTIVCDEEEIMekRIVSGVAYSRDEAKITLL--GLPDHPGVSSQIFGRLAEANVNVDMI 302
                                       *****9997433323459*****955533348*****************..99************************ PP

                         TIGR00656 301 sqtese....tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleeknin 373
                                       +q++++     +++++v ++d+++a+++ ++ ++++++e + v+ed+a+vs++g+g++++ Gva+ +f+al+eknin
  FitnessBrowser__Caulo:CCNA_00886 303 VQSRARsadtANMEFTVGKRDATRAVEIVQAAQKEIGFEAVAVNEDVAKVSVIGVGMRSHAGVAQSMFQALAEKNIN 379
                                       ****99989889***************************************************************** PP

                         TIGR00656 374 ilmisssetkisvlvdekdaekavrklhekle 405
                                       i  is+se+kisvl+d +++e avr+lh+++ 
  FitnessBrowser__Caulo:CCNA_00886 380 IQVISTSEIKISVLIDAAYTELAVRALHAVYG 411
                                       ****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (415 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.24
//
[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 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