GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asp-kinase in Azospirillum brasilense Sp245

Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate AZOBR_RS18890 AZOBR_RS18890 aspartate kinase

Query= SwissProt::A4VJB4
         (412 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS18890 AZOBR_RS18890 aspartate
           kinase
          Length = 411

 Score =  441 bits (1135), Expect = e-128
 Identities = 237/411 (57%), Positives = 303/411 (73%), Gaps = 7/411 (1%)

Query: 1   MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60
           MA IV KFGGTSVG ++RI+ VA KV++    G  + VVVSAMSG TN+L+     I + 
Sbjct: 1   MARIVLKFGGTSVGDIDRIKNVARKVEQEVKAGHQVAVVVSAMSGVTNQLVKYCNDIDKL 60

Query: 61  PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120
              RE D +V++GEQVT  LLA+AL   G+ A S+ G Q+ I +D  H KARI+ ID   
Sbjct: 61  HDAREYDAIVASGEQVTSGLLAIALQSLGIQARSWLGWQIPIYSDETHGKARIVSIDTAE 120

Query: 121 IQRDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180
           + + +  G V VVAGFQGV E G ITTLGRGGSDT+ VALAAALKAD C IYTDVDGVYT
Sbjct: 121 LDKRMNTGEVAVVAGFQGVTETGRITTLGRGGSDTSAVALAAALKADRCDIYTDVDGVYT 180

Query: 181 TDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQEG----- 235
           TDPR+V KA++L KIT+EEMLE+AS G+KVLQ R+VE A  + V ++VL SF+E      
Sbjct: 181 TDPRIVTKARKLSKITYEEMLELASQGAKVLQTRSVEMAMNHRVRVQVLSSFEEAAGSAL 240

Query: 236 PGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIV 295
           PGTL+ +DE+E +E+ ++SGIA++RDEAK+T+ GV D PGVA  I GP++ A V VDMIV
Sbjct: 241 PGTLV-VDEDEIVEKEVVSGIAYSRDEAKITLIGVADRPGVAASIFGPLTDAAVNVDMIV 299

Query: 296 QNVAHD-NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHA 354
           QNV+ D  +TD TFTV + D   A++VL+   AE+  +  + D N+ KVS++GVGMRSHA
Sbjct: 300 QNVSEDGKSTDMTFTVGKADIARAVKVLEDAQAELNYKRIVSDANVVKVSVIGVGMRSHA 359

Query: 355 GVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 405
           GVA RMF+ALA + INIQ+ISTSEIK+SV+I E+Y ELA+RALHTA+ LDA
Sbjct: 360 GVAQRMFKALADKGINIQVISTSEIKISVLIAEEYAELALRALHTAYGLDA 410


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: 437
Number of extensions: 22
Number of successful extensions: 4
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: 411
Length adjustment: 31
Effective length of query: 381
Effective length of database: 380
Effective search space:   144780
Effective search space used:   144780
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 AZOBR_RS18890 AZOBR_RS18890 (aspartate kinase)
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.6061.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-132  428.6  18.2   1.5e-132  428.4  18.2    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS18890  AZOBR_RS18890 aspartate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS18890  AZOBR_RS18890 aspartate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.4  18.2  1.5e-132  1.5e-132       4     405 ..       4     407 ..       1     409 [. 0.96

  Alignments for each domain:
  == domain 1  score: 428.4 bits;  conditional E-value: 1.5e-132
                                 TIGR00656   4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 
                                               iV KFGGtsvg+++rik++a++v +e+k g++v VVvSAms+vt++lv+        + i +    re 
  lcl|FitnessBrowser__azobra:AZOBR_RS18890   4 IVLKFGGTSVGDIDRIKNVARKVEQEVKAGHQVAVVVSAMSGVTNQLVKYC------NDIDKLHDAREY 66 
                                               9**************************************************......788888899*** PP

                                 TIGR00656  73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141
                                               d +v+ GE+++s ll+ al+ lg +a++  g++ +i  d+++g+A+i +++t  +L ++++ g + vva
  lcl|FitnessBrowser__azobra:AZOBR_RS18890  67 DAIVASGEQVTSGLLAIALQSLGIQARSWLGWQIPIYSDETHGKARIVSIDT-AELDKRMNTGEVAVVA 134
                                               ****************************************************.9*************** PP

                                 TIGR00656 142 GFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalel 210
                                               GF+G te G+iTtLGRGGSD++A++laaalkAdr++iyTDV+GvyttDPr+v +a+k+ ki+yeE+lel
  lcl|FitnessBrowser__azobra:AZOBR_RS18890 135 GFQGVTETGRITTLGRGGSDTSAVALAAALKADRCDIYTDVDGVYTTDPRIVTKARKLSKITYEEMLEL 203
                                               ********************************************************************* PP

                                 TIGR00656 211 AtlGakvlhpralelaveakvpilvrsskeke.....egTlitn..kkensslvkaialeknvarltve 272
                                               A++Gakvl+ r++e+a++  v + v ss+e+       gTl+++  +  ++++v++ia++++ a++t+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS18890 204 ASQGAKVLQTRSVEMAMNHRVRVQVLSSFEEAagsalPGTLVVDedEIVEKEVVSGIAYSRDEAKITLI 272
                                               ****************************997521124579999955455669***************** PP

                                 TIGR00656 273 gegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesl 337
                                                 g+++++g++a if+ L ++ +nvd+i+q  se    t+++++v + d+ +a+k+L++ + +++++++
  lcl|FitnessBrowser__azobra:AZOBR_RS18890 273 --GVADRPGVAASIFGPLTDAAVNVDMIVQNVSEdgksTDMTFTVGKADIARAVKVLEDAQAELNYKRI 339
                                               ..9******************************9999******************************** PP

                                 TIGR00656 338 eveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405
                                                 + ++ +vs++g+g++++ Gva+++fkal++k+ini  is+se+kisvl+ e++ae a r+lh ++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS18890 340 VSDANVVKVSVIGVGMRSHAGVAQRMFKALADKGINIQVISTSEIKISVLIAEEYAELALRALHTAYG 407
                                               ****************************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (411 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: 7.12
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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