Alignments for a candidate for asp-kinase in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pseudomonas stutzeri RCH2

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate GFF2932 Psest_2988 aspartate kinase, monofunctional class

Query= SwissProt::A4VJB4
         (412 letters)



>FitnessBrowser__psRCH2:GFF2932
          Length = 412

 Score =  778 bits (2008), Expect = 0.0
 Identities = 408/412 (99%), Positives = 410/412 (99%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           MALIVQKFGGTSVGTVERIEQVAEKVKKFR+GGDDIVVVVSAMSGETNRLIDLAKQISEQ
Sbjct: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFREGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
           PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQID QR
Sbjct: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDGQR 120

Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT
Sbjct: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180

Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240
           TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI
Sbjct: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEGPGTLI 240

Query: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300
           TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH
Sbjct: 241 TLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAH 300

Query: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRM 360
           DNTTDFTFTVHRNDYNNALQVLQGIAAEMGARE IGDT+IAKVSIVGVGMRSHAGVASRM
Sbjct: 301 DNTTDFTFTVHRNDYNNALQVLQGIAAEMGAREVIGDTDIAKVSIVGVGMRSHAGVASRM 360

Query: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPAGNTAE 412
           FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPAGNTAE
Sbjct: 361 FEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPAGNTAE 412


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: 726
Number of extensions: 15
Number of successful extensions: 1
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: 412
Length adjustment: 31
Effective length of query: 381
Effective length of database: 381
Effective search space:   145161
Effective search space used:   145161
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 GFF2932 Psest_2988 (aspartate kinase, monofunctional class)
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.19479.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.3e-137  443.0  14.3     6e-137  442.9  14.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2932  Psest_2988 aspartate kinase, mon


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2932  Psest_2988 aspartate kinase, monofunctional class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.9  14.3    6e-137    6e-137       1     406 [.       1     403 [.       1     404 [. 0.98

  Alignments for each domain:
  == domain 1  score: 442.9 bits;  conditional E-value: 6e-137
                           TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdel 75 
                                         + liVqKFGGtsvg +eri+++a++v+k  + g++ vVVvSAms++t++l++la      ++is+++ pre d +
  lcl|FitnessBrowser__psRCH2:GFF2932   1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREGGDDIVVVVSAMSGETNRLIDLA------KQISEQPVPRELDVM 69 
                                         579***************************************************......9************** PP

                           TIGR00656  76 vsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeG 150
                                         vs+GE++++all++al ++gv a++++g++  ilTd+ +++A+i +++  +r+   ++ g +vvvaGF+G +e+G
  lcl|FitnessBrowser__psRCH2:GFF2932  70 VSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDG-QRIQRDIKAGRVVVVAGFQGVDEKG 143
                                         *************************************************.************************* PP

                           TIGR00656 151 eiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralel 225
                                         +iTtLGRGGSD+t ++laaalkAd+++iyTDV+GvyttDPrvv +a+++dki++eE+le+A+lG kvl+ ra+e+
  lcl|FitnessBrowser__psRCH2:GFF2932 144 NITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEF 218
                                         *************************************************************************** PP

                           TIGR00656 226 aveakvpilvrsskekeegTlitn....kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeein 296
                                         a +++vp++v +s+++  gTlit     ++e++ ++++ia++++ a+lt++  g+ + +g++ +i + ++ +++ 
  lcl|FitnessBrowser__psRCH2:GFF2932 219 AGKYSVPLRVLHSFQEGPGTLITLdeeeSMEQP-IISGIAFNRDEAKLTIR--GVPDTPGVAFKILGPISAANVE 290
                                         **********************98555566666.*****************..9********************* PP

                           TIGR00656 297 vdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkale 368
                                         vd+i+q  ++   t+ +++v+++d ++a ++L+    +++ +++  + d+a+vsivg+g++++ Gvas++f+al+
  lcl|FitnessBrowser__psRCH2:GFF2932 291 VDMIVQNVAHdntTDFTFTVHRNDYNNALQVLQGIAAEMGAREVIGDTDIAKVSIVGVGMRSHAGVASRMFEALA 365
                                         ******99988889************************************************************* PP

                           TIGR00656 369 ekninilmisssetkisvlvdekdaekavrklheklee 406
                                         ++nini mis+se+k+sv+++ek++e avr+lh ++e+
  lcl|FitnessBrowser__psRCH2:GFF2932 366 KENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFEL 403
                                         ***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (412 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.85
//
[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