GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Lentibacillus jeotgali Grbi

Align aspartokinase I (alpha and beta subunits) (EC 2.7.2.4) (characterized)
to candidate WP_010530678.1 ON01_RS08880 aspartate kinase

Query= metacyc::BSU16760-MONOMER
         (404 letters)



>NCBI__GCF_000224785.1:WP_010530678.1
          Length = 410

 Score =  491 bits (1265), Expect = e-143
 Identities = 248/403 (61%), Positives = 314/403 (77%)

Query: 1   MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60
           M+I+VQKFGGTSV+ +  R   + HIK A+   YK+VVVVSA+GRK  PYATDSLL L+ 
Sbjct: 1   MQILVQKFGGTSVQTEDNRTHVIQHIKNALMNDYKIVVVVSALGRKPAPYATDSLLDLVD 60

Query: 61  GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120
             ++  S RE D+L+SCGETI+SVV ++ L  N + A ALTGAQAGF+TND    AKI E
Sbjct: 61  FPKNYNSNRELDILMSCGETIASVVLSNELQKNHISATALTGAQAGFVTNDDFNQAKIKE 120

Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180
           +KP+R+ +    HD VVVAGFQG +  G+ TTIGRGGSDT+AAA+GAAV+AE I+IFTDV
Sbjct: 121 VKPDRVLNEFKEHDVVVVAGFQGQSSDGEITTIGRGGSDTTAAAMGAAVNAERIEIFTDV 180

Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240
            G+MTADP VV +A+PL +VTYTEICNLAYQGAKVI PRAVEIAMQAK+P+RVRSTY  D
Sbjct: 181 NGIMTADPSVVSSARPLDIVTYTEICNLAYQGAKVIHPRAVEIAMQAKIPMRVRSTYVED 240

Query: 241 KGTLVTSHHSSKVGSDVFERLITGIAHVKDVTQFKVPAKIGQYNVQTEVFKAMANAGISV 300
           +GTL+T+    ++G+D+ +RLITGIAH+  +TQ  V  K   + +Q++VFKAMA AGISV
Sbjct: 241 EGTLITASRIQEMGTDIPDRLITGIAHMSSITQISVQTKEETHRLQSDVFKAMAEAGISV 300

Query: 301 DFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVTSKIV 360
           DF NI+P+ ++YTV    T+ A  IL  +G+ P +T+NCAKVSAVGAG+ GVPGV SKIV
Sbjct: 301 DFINISPNGVIYTVPDTHTKKAVHILETLGFYPEITKNCAKVSAVGAGMTGVPGVASKIV 360

Query: 361 SALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEVFELS 403
            +L++  + ILQSADSHTTIWVL+HE D+ PAVNALH+VF L+
Sbjct: 361 QSLTDAGVQILQSADSHTTIWVLIHEDDLKPAVNALHDVFALN 403


Lambda     K      H
   0.316    0.131    0.364 

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: 523
Number of extensions: 11
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: 404
Length of database: 410
Length adjustment: 31
Effective length of query: 373
Effective length of database: 379
Effective search space:   141367
Effective search space used:   141367
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 WP_010530678.1 ON01_RS08880 (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.2643585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-131  422.7   8.9   9.2e-131  422.5   8.9    1.0  1  NCBI__GCF_000224785.1:WP_010530678.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010530678.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.5   8.9  9.2e-131  9.2e-131       1     406 [.       1     402 [.       1     403 [. 0.97

  Alignments for each domain:
  == domain 1  score: 422.5 bits;  conditional E-value: 9.2e-131
                             TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 
                                           +++ VqKFGGtsv+  +++ ++ ++++++l++++k vVVvSA++++   +++ + ll+l++  ++  s+re d
  NCBI__GCF_000224785.1:WP_010530678.1   1 MQILVQKFGGTSVQTEDNRTHVIQHIKNALMNDYKIVVVVSALGRKPAPYATDS-LLDLVDFPKNYNSNRELD 72 
                                           6899**************************************************.9***************** PP

                             TIGR00656  74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146
                                            l+s+GE+++s++ls+ l+++   a+al+g++ag++T+d f++Akike+++  r+l+  +e+++vvvaGF+G+
  NCBI__GCF_000224785.1:WP_010530678.1  73 ILMSCGETIASVVLSNELQKNHISATALTGAQAGFVTNDDFNQAKIKEVKP-DRVLNEFKEHDVVVVAGFQGQ 144
                                           ***************************************************.999999*************** PP

                             TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219
                                            ++GeiTt+GRGGSD+tAa+++aa++A+r+ei+TDV+G++t+DP vv++a+++d ++y+E+++lA++Gakv+h
  NCBI__GCF_000224785.1:WP_010530678.1 145 SSDGEITTIGRGGSDTTAAAMGAAVNAERIEIFTDVNGIMTADPSVVSSARPLDIVTYTEICNLAYQGAKVIH 217
                                           ************************************************************************* PP

                             TIGR00656 220 pralelaveakvpilvrsskekeegTlitn....kkens...slvkaialeknvarltvegegmlgkrgilae 285
                                           pra+e+a++ak+p++vrs++ ++egTlit+    ++ ++   +l+++ia+   +++++v+   + + + +++ 
  NCBI__GCF_000224785.1:WP_010530678.1 218 PRAVEIAMQAKIPMRVRSTYVEDEGTLITAsriqEMGTDipdRLITGIAHMSSITQISVQ--TKEETHRLQSD 288
                                           ******************************6665444447799*****************..88888999*** PP

                             TIGR00656 286 ifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapG 358
                                           +fka+ae++i+vd+i++++  + + ++v ++ +++a+++L++          e+ +++a+vs+vgag++++pG
  NCBI__GCF_000224785.1:WP_010530678.1 289 VFKAMAEAGISVDFINISP--NGVIYTVPDTHTKKAVHILETLGFYP-----EITKNCAKVSAVGAGMTGVPG 354
                                           *******************..*********************97443.....5889***************** PP

                             TIGR00656 359 vaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406
                                           vas+i++ l + +++il++++s+t+i+vl++e d++ av++lh+++ +
  NCBI__GCF_000224785.1:WP_010530678.1 355 VASKIVQSLTDAGVQILQSADSHTTIWVLIHEDDLKPAVNALHDVFAL 402
                                           ********************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (410 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.15
//
[ok]

This GapMind analysis is from Jul 26 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:

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