Alignments for a candidate for asp-kinase in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Phaeobacter inhibens BS107

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate GFF2319 PGA1_c23510 aspartokinase LysC

Query= SwissProt::A4VJB4
         (412 letters)



>FitnessBrowser__Phaeo:GFF2319
          Length = 412

 Score =  399 bits (1026), Expect = e-116
 Identities = 217/413 (52%), Positives = 292/413 (70%), Gaps = 7/413 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           M ++V KFGGTSV  ++RI + A++V      G +++V+VSAMSG+TN L+    + S  
Sbjct: 1   MPVLVMKFGGTSVANLDRIRRAAKRVGVEVAKGYNVIVIVSAMSGKTNELVGWVNETSPL 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
              RE D +VS+GE VT  L+A+ L +  +PA S+ G QV + T SAH++ARI +I  + 
Sbjct: 61  FDAREYDAVVSSGENVTAGLMALTLQEMDIPARSWQGWQVPLKTTSAHSQARIEEIPPEN 120

Query: 121 IQRDIKAG-RVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179
           I      G RV VVAGFQG+  +G ITTLGRGGSDTT VA AAA +A+ C IYTDVDGVY
Sbjct: 121 INAKFGEGMRVAVVAGFQGISPEGRITTLGRGGSDTTAVAFAAAFEAERCDIYTDVDGVY 180

Query: 180 TTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQE---GP 236
           TTDPR+  KA++LDKI FEEMLE+ASLG+KVLQ R+VE A +Y V LRVL SF+E     
Sbjct: 181 TTDPRICDKARKLDKIAFEEMLELASLGAKVLQTRSVELAMRYKVKLRVLSSFEEQSDEA 240

Query: 237 GTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQ 296
           GTL+  DEEE ME  +++G+A++RDEAKLT++ V D PG+A  I   +S A V VDMIVQ
Sbjct: 241 GTLV-CDEEEIMESNVVAGVAYSRDEAKLTVQSVADRPGIAAHIFTALSEAGVNVDMIVQ 299

Query: 297 NVAHDNTTDFTFTVHRNDYNNALQVLQGI--AAEMGAREAIGDTNIAKVSIVGVGMRSHA 354
           +++ +  TD TF+   +    A Q LQ +    E+   E + D ++AKVS+VG+GMRS +
Sbjct: 300 DISDEGRTDMTFSCPTDQVVRAEQALQAVKEKGELNYAELLADRDVAKVSVVGIGMRSQS 359

Query: 355 GVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPA 407
           GVA++MF+ L+ E INI++I+TSEIK+SV+I+ KY+ELAV+ALH AFELD  A
Sbjct: 360 GVAAKMFKVLSDEGINIKVITTSEIKISVLIDRKYMELAVQALHDAFELDKAA 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: 417
Number of extensions: 10
Number of successful extensions: 5
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 GFF2319 PGA1_c23510 (aspartokinase LysC)
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.11049.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-129  418.5   7.5   1.7e-129  418.3   7.5    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2319  PGA1_c23510 aspartokinase LysC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2319  PGA1_c23510 aspartokinase LysC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.3   7.5  1.7e-129  1.7e-129       3     406 ..       3     408 ..       1     409 [. 0.95

  Alignments for each domain:
  == domain 1  score: 418.3 bits;  conditional E-value: 1.7e-129
                          TIGR00656   3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelvsv 78 
                                        + V+KFGGtsv++ +ri++aak+v  e+ +g++v+V+vSAms++t+elv  +      + +s     re d +vs 
  lcl|FitnessBrowser__Phaeo:GFF2319   3 VLVMKFGGTSVANLDRIRRAAKRVGVEVAKGYNVIVIVSAMSGKTNELVGWV------NETSPLFDAREYDAVVSS 72 
                                        78**************************************************......8999999*********** PP

                          TIGR00656  79 GEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegi.ivvvaGFiGateeGeiT 153
                                        GE +++ l++  l+e +  a++ +g++ ++ T + + +A+i+e+ + e++     eg+ + vvaGF+G   eG+iT
  lcl|FitnessBrowser__Phaeo:GFF2319  73 GENVTAGLMALTLQEMDIPARSWQGWQVPLKTTSAHSQARIEEIPP-ENINAKFGEGMrVAVVAGFQGISPEGRIT 147
                                        **********************************************.88888888875489*************** PP

                          TIGR00656 154 tLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelavea 229
                                        tLGRGGSD+tA++ aaa +A+r++iyTDV+GvyttDPr+ ++a+k+dki++eE+lelA+lGakvl+ r++ela+++
  lcl|FitnessBrowser__Phaeo:GFF2319 148 TLGRGGSDTTAVAFAAAFEAERCDIYTDVDGVYTTDPRICDKARKLDKIAFEEMLELASLGAKVLQTRSVELAMRY 223
                                        **************************************************************************** PP

                          TIGR00656 230 kvpilvrsskeke...egTlitnkkens..slvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdli 300
                                        kv+++v ss+e++   +gTl+++++e    ++v ++a++++ a+ltv+  ++++++gi+a+if+aL+e+++nvd+i
  lcl|FitnessBrowser__Phaeo:GFF2319 224 KVKLRVLSSFEEQsdeAGTLVCDEEEIMesNVVAGVAYSRDEAKLTVQ--SVADRPGIAAHIFTALSEAGVNVDMI 297
                                        ********998654468*****954433236*****************..************************** PP

                          TIGR00656 301 sqtese...tsislvvdeedvdeakkaLkeesgaae..lesleveedlavvsivgaglveapGvaseifkaleekn 371
                                        +q  s+   t+++++  + +v +a++aL++++++ e  + +l  ++d+a+vs+vg g+++++Gva+++fk+l++++
  lcl|FitnessBrowser__Phaeo:GFF2319 298 VQDISDegrTDMTFSCPTDQVVRAEQALQAVKEKGElnYAELLADRDVAKVSVVGIGMRSQSGVAAKMFKVLSDEG 373
                                        **9987788********************99877666699999********************************* PP

                          TIGR00656 372 inilmisssetkisvlvdekdaekavrklheklee 406
                                        ini+ i++se+kisvl+d k++e av++lh+++e+
  lcl|FitnessBrowser__Phaeo:GFF2319 374 INIKVITTSEIKISVLIDRKYMELAVQALHDAFEL 408
                                        *********************************97 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.25
//
[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