GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Clostridium tyrobutyricum FAM22553

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_017751807.1 PN53_RS01895 biosynthetic-type acetolactate synthase large subunit

Query= metacyc::MONOMER-11900
         (599 letters)



>NCBI__GCF_000816635.1:WP_017751807.1
          Length = 559

 Score =  486 bits (1251), Expect = e-141
 Identities = 254/573 (44%), Positives = 366/573 (63%), Gaps = 18/573 (3%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHH--SDLIHLLTRHEQAAAHAADGYA 58
           M GA+ +++ L    V+ +FGYPGGA+LP YDAL+     + H++T HEQ A+HAADGYA
Sbjct: 1   MKGAKMLLECLVQHGVDTIFGYPGGAVLPIYDALYDMKDKINHIITAHEQGASHAADGYA 60

Query: 59  RASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118
           R++GKVGV + TSGPGATN VTG+ATA+ DS P++   GQVP  L+G D+FQE++   + 
Sbjct: 61  RSTGKVGVALATSGPGATNTVTGIATAYMDSVPIIVFAGQVPVSLVGKDSFQEVNIRSIT 120

Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178
             I K  F I K   I  +   AF+IA +GR GPV I++PK+VQ  E  I +  + S   
Sbjct: 121 GTITKKTFTIDKVENIKSVIDEAFKIATSGRKGPVVIEVPKNVQVSE--ISEMSLNSIEN 178

Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238
            + Y+  +  H   + KAIK+I +++RP++ AGGGV+ SGA +EL K V+ L+ P+  +L
Sbjct: 179 ELIYDLFSNKHENALNKAIKIIENSERPMVYAGGGVVSSGAEDELSKFVDKLDTPISCSL 238

Query: 239 MGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKII 298
           MG G   ++     GM+GMHGT  +N  +++ D+LI+IG RFSDR+   + +FA NA+II
Sbjct: 239 MGTGAFPQDRDNYTGMLGMHGTHTSNQAINDCDLLIAIGARFSDRVISKVSTFAKNARII 298

Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358
           HIDID  E GKN++VD+ I GD K IL++        +N   K  N     S+W+  + S
Sbjct: 299 HIDIDEKEFGKNIDVDLTIKGDIKNILEK--------LNSSIKNQNH----SKWMRKIIS 346

Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418
            KK+    ++ +D   K     + ++  + +L    + I+TT+VGQNQ+W A YFK   P
Sbjct: 347 SKKNEELKIENNDSEKKDYVSPRHIIETLYELT-GGDCIVTTEVGQNQIWTAQYFKFLKP 405

Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478
           R+FL+SGGLGTMGFG  +AIGA V  PD +VI + GDG F MNC EL TI++Y +PV+  
Sbjct: 406 RTFLTSGGLGTMGFGLGAAIGACVGNPDKRVINVAGDGSFKMNCNELATISKYKLPVIQL 465

Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538
           + +N +LGMV+QWQ +FY +R C        D +KL E+YGIK  +IE+ NEI + L+ A
Sbjct: 466 VLNNNSLGMVHQWQEMFYNRRYCFTELTDDVDILKLGEAYGIKTLKIENNNEIEDCLRFA 525

Query: 539 INCDEPYLLDFAID-PSSALSMVPPGAKLTNII 570
           +   EP +++ +ID       +VPPGA +T+ I
Sbjct: 526 LEKREPIIIECSIDINEKVFPIVPPGASITDSI 558


Lambda     K      H
   0.319    0.137    0.405 

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: 855
Number of extensions: 40
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: 599
Length of database: 559
Length adjustment: 36
Effective length of query: 563
Effective length of database: 523
Effective search space:   294449
Effective search space used:   294449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_017751807.1 PN53_RS01895 (biosynthetic-type acetolactate synthase large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# 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/TIGR00118.hmm
# target sequence database:        /tmp/gapView.2691264.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-221  720.8   1.4   6.1e-221  720.6   1.4    1.0  1  NCBI__GCF_000816635.1:WP_017751807.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_017751807.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  720.6   1.4  6.1e-221  6.1e-221       1     553 [.       1     557 [.       1     559 [] 0.97

  Alignments for each domain:
  == domain 1  score: 720.6 bits;  conditional E-value: 6.1e-221
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                           +kga++l+e l ++gv+t+fGyPGGavlpiydaly  +++++hi++ heq+a+haadGyar++GkvGv+lats
  NCBI__GCF_000816635.1:WP_017751807.1   1 MKGAKMLLECLVQHGVDTIFGYPGGAVLPIYDALYdmKDKINHIITAHEQGASHAADGYARSTGKVGVALATS 73 
                                           89*********************************9999********************************** PP

                             TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafei 144
                                           GPGatn+vtgiatay+dsvP++v++Gqv+ sl+G+d+fqe++i  it ++tk +f + k+e++ +++ eaf+i
  NCBI__GCF_000816635.1:WP_017751807.1  74 GPGATNTVTGIATAYMDSVPIIVFAGQVPVSLVGKDSFQEVNIRSITGTITKKTFTIDKVENIKSVIDEAFKI 146
                                           ************************************************************************* PP

                             TIGR00118 145 astGrPGPvlvdlPkdvteaeieleveekvelp.gykptvkghklqikkaleliekakkPvllvGgGviiaea 216
                                           a++Gr GPv++++Pk+v+ +ei+    +++e    y +  + h++ ++ka+++ie++++P++++GgGv+ ++a
  NCBI__GCF_000816635.1:WP_017751807.1 147 ATSGRKGPVVIEVPKNVQVSEISEMSLNSIENElIYDLFSNKHENALNKAIKIIENSERPMVYAGGGVVSSGA 219
                                           *********************999888777654279************************************* PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           ++el +++++l+ p+ ++l+G Gafp+d  +  gmlGmhGt+++n a++++dllia+Garf+drv +++++fa
  NCBI__GCF_000816635.1:WP_017751807.1 220 EDELSKFVDKLDTPISCSLMGTGAFPQDRDNYTGMLGMHGTHTSNQAINDCDLLIAIGARFSDRVISKVSTFA 292
                                           ************************************************************************* PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeees.. 360
                                           ++a+iihidid +e gkn+ vd++i Gd k++le+l + +k++++++  W++ki + kk+  lk+++++++  
  NCBI__GCF_000816635.1:WP_017751807.1 293 KNARIIHIDIDEKEFGKNIDVDLTIKGDIKNILEKLNSSIKNQNHSK--WMRKIISSKKNEELKIENNDSEkk 363
                                           **************************************999887776..*********999999775432212 PP

                             TIGR00118 361 ..ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431
                                             + P+++i++l++l+ ++ ivtt+vGq+q+w+aq++k+ kpr+f+tsgGlGtmGfGl aa+Ga v++p++ v
  NCBI__GCF_000816635.1:WP_017751807.1 364 dyVSPRHIIETLYELTGGDCIVTTEVGQNQIWTAQYFKFLKPRTFLTSGGLGTMGFGLGAAIGACVGNPDKRV 436
                                           4599********************************************************************* PP

                             TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504
                                           ++v+Gdgsf+mn++el+ti++y++pv+ ++lnn+ lGmv+qWqe+fy++ry  t+l+ +  d+ kl eayG+k
  NCBI__GCF_000816635.1:WP_017751807.1 437 INVAGDGSFKMNCNELATISKYKLPVIQLVLNNNSLGMVHQWQEMFYNRRYCFTELT-DDVDILKLGEAYGIK 508
                                           *********************************************************.699************ PP

                             TIGR00118 505 giriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                           +++ie+++e+e+ l+ ale++ep++++ ++d +e+v+P+v+pGa++++ 
  NCBI__GCF_000816635.1:WP_017751807.1 509 TLKIENNNEIEDCLRFALEKREPIIIECSIDINEKVFPIVPPGASITDS 557
                                           ********************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (559 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 24.51
//
[ok]

This GapMind analysis is from Jul 25 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