GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Azohydromonas australica DSM 1124

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_028999235.1 H537_RS0119920 acetolactate synthase 3 catalytic subunit

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_000430725.1:WP_028999235.1
          Length = 590

 Score =  906 bits (2341), Expect = 0.0
 Identities = 439/573 (76%), Positives = 500/573 (87%), Gaps = 1/573 (0%)

Query: 14  SAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAA 73
           S + E+ G+EILV +L  EGV+Y+WGYPGG+VLYIYD L+KQ   +H+LVRHEQAAVHAA
Sbjct: 18  SPSAELNGSEILVRSLQAEGVKYLWGYPGGSVLYIYDALYKQDSIQHVLVRHEQAAVHAA 77

Query: 74  DGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDT 133
           DGYARATG+VGVALVTSGPGVTNAVTGIATAY+DSIPMV+ITG VPT AIG DAFQECDT
Sbjct: 78  DGYARATGEVGVALVTSGPGVTNAVTGIATAYMDSIPMVIITGQVPTAAIGLDAFQECDT 137

Query: 134 VGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSI 193
           VGITRPIVKHNFLVKDVR+LA T+KKAF IA TGRPGPVVVDIPKDVS     + YP  +
Sbjct: 138 VGITRPIVKHNFLVKDVRELALTLKKAFHIARTGRPGPVVVDIPKDVSLKTAPFSYPDKV 197

Query: 194 DMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNT 253
           +MRSYNPV KGH GQIRKAV LL  A+RPYIY+GGGVVLANA+ ELR+LA L G+P TNT
Sbjct: 198 EMRSYNPVRKGHGGQIRKAVQLLLQAKRPYIYSGGGVVLANAAAELRELADLLGYPCTNT 257

Query: 254 LMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARK 313
           LMGLGA P +  +F+GMLGMHGTYEANM MQ+CDVL+A+GARFDDRVIGNPAHF S  RK
Sbjct: 258 LMGLGAIPASDPKFLGMLGMHGTYEANMTMQHCDVLLAVGARFDDRVIGNPAHFASVERK 317

Query: 314 IIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRS 373
           I+H+DIDPSSISKRVKVDIPIVG+VK+VLQELIAQI+ +  +P ++A+A WW Q+  WR 
Sbjct: 318 IVHVDIDPSSISKRVKVDIPIVGDVKEVLQELIAQIREAQQRPDQQAMAHWWSQVNGWRQ 377

Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432
            +CL Y  SSE+IKPQYVV+K+ ELT+G D +I SDVGQHQM+AAQFY F+EPRRWINSG
Sbjct: 378 RECLAYKNSSEVIKPQYVVQKLAELTRGRDTYITSDVGQHQMFAAQFYGFEEPRRWINSG 437

Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492
           GLGTMGVGLPYAMGIK A PE +V  ITGEGSIQMCIQELSTC QY TPVK+ SLNN YL
Sbjct: 438 GLGTMGVGLPYAMGIKLAKPESDVFCITGEGSIQMCIQELSTCQQYKTPVKVISLNNRYL 497

Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552
           GMVRQWQE++Y+ RYSHSYMDALPDFVKLAEAYGHVG+++E+ +DVEPALREA RL DRT
Sbjct: 498 GMVRQWQELDYEGRYSHSYMDALPDFVKLAEAYGHVGLKIERPADVEPALREAIRLTDRT 557

Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           VFLD +TDPTENVWPMV+AGKGISEMLLG+EDL
Sbjct: 558 VFLDIRTDPTENVWPMVKAGKGISEMLLGSEDL 590


Lambda     K      H
   0.319    0.135    0.407 

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: 1051
Number of extensions: 31
Number of successful extensions: 2
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: 585
Length of database: 590
Length adjustment: 37
Effective length of query: 548
Effective length of database: 553
Effective search space:   303044
Effective search space used:   303044
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate WP_028999235.1 H537_RS0119920 (acetolactate synthase 3 catalytic 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.3828266.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-257  840.0   0.1   4.8e-257  839.8   0.1    1.0  1  NCBI__GCF_000430725.1:WP_028999235.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_028999235.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  839.8   0.1  4.8e-257  4.8e-257       2     554 ..      24     584 ..      23     587 .. 0.98

  Alignments for each domain:
  == domain 1  score: 839.8 bits;  conditional E-value: 4.8e-257
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           +g+eilv+sl++egv++++GyPGG+vl iydaly ++ ++h+lvrheqaa+haadGyara+G+vGv+l+tsGP
  NCBI__GCF_000430725.1:WP_028999235.1  24 NGSEILVRSLQAEGVKYLWGYPGGSVLYIYDALYkQDSIQHVLVRHEQAAVHAADGYARATGEVGVALVTSGP 96 
                                           799*******************************9999*********************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           G tn+vtgiatay+ds+P+v++tGqv+t++iG dafqe+d +Git+p++kh+flvk++++l+ +lk+af+ia 
  NCBI__GCF_000430725.1:WP_028999235.1  97 GVTNAVTGIATAYMDSIPMVIITGQVPTAAIGLDAFQECDTVGITRPIVKHNFLVKDVRELALTLKKAFHIAR 169
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219
                                           tGrPGPv+vd+Pkdv+ ++  +++++kve+++y+p  kgh  qi+ka++l+ +ak+P ++ GgGv+ a+a +e
  NCBI__GCF_000430725.1:WP_028999235.1 170 TGRPGPVVVDIPKDVSLKTAPFSYPDKVEMRSYNPVRKGHGGQIRKAVQLLLQAKRPYIYSGGGVVLANAAAE 242
                                           ************************************************************************* PP

                             TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap.e 291
                                           l+ela+ l  p t tl+GlGa+p+ +p++lgmlGmhGt+ean++++++d+l+avGarfddrv gn a+fa+ e
  NCBI__GCF_000430725.1:WP_028999235.1 243 LRELADLLGYPCTNTLMGLGAIPASDPKFLGMLGMHGTYEANMTMQHCDVLLAVGARFDDRVIGNPAHFASvE 315
                                           *********************************************************************9757 PP

                             TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkekeWlekieewkkeyilkldeeee 359
                                            ki+h+didP++i+k vkvdipivGd+k+vl+el+++++e      ++   +W+++++ w+++ +l++++++e
  NCBI__GCF_000430725.1:WP_028999235.1 316 RKIVHVDIDPSSISKRVKVDIPIVGDVKEVLQELIAQIREAqqrpdQQAMAHWWSQVNGWRQRECLAYKNSSE 388
                                           89***********************************999866663333445********************* PP

                             TIGR00118 360 sikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431
                                            ikPq+v+++l +l+++ ++++t+dvGqhqm+aaqfy +++pr++i+sgGlGtmG GlP a+G+k+akpe++v
  NCBI__GCF_000430725.1:WP_028999235.1 389 VIKPQYVVQKLAELTRGrDTYITSDVGQHQMFAAQFYGFEEPRRWINSGGLGTMGVGLPYAMGIKLAKPESDV 461
                                           ***************9989****************************************************** PP

                             TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504
                                            ++tG+gs+qm +qelst+++y++pvk++ lnn++lGmv+qWqel ye+rys++++ + lpdfvklaeayG++
  NCBI__GCF_000430725.1:WP_028999235.1 462 FCITGEGSIQMCIQELSTCQQYKTPVKVISLNNRYLGMVRQWQELDYEGRYSHSYMDA-LPDFVKLAEAYGHV 533
                                           *********************************************************5.************** PP

                             TIGR00118 505 giriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554
                                           g++ie+p+++e +l+ea++ + + v+ld++ d +e+v+Pmv  G+g++e++
  NCBI__GCF_000430725.1:WP_028999235.1 534 GLKIERPADVEPALREAIRLTdRTVFLDIRTDPTENVWPMVKAGKGISEML 584
                                           ******************976599*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (590 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 15.86
//
[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