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.4271.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.23
//
[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:

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:

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:

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:

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