Alignments for a candidate for ilvI in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Acidovorax sp. GW101-3H11

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate Ac3H11_525 Acetolactate synthase large subunit (EC 2.2.1.6)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_525
          Length = 597

 Score =  894 bits (2311), Expect = 0.0
 Identities = 435/578 (75%), Positives = 498/578 (86%), Gaps = 3/578 (0%)

Query: 11  SNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAV 70
           S +S + +++G+EIL+ +L  E V+Y+WGYPGGAVLYIYD L+KQ   +H+LVRHEQAAV
Sbjct: 20  SPASGSQDLMGSEILIKSLQAENVQYIWGYPGGAVLYIYDALYKQDTIQHVLVRHEQAAV 79

Query: 71  HAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQE 130
           HAADGYARATG+VGVALVTSGPG+TNAVTGIATAY+DSIPMV+I+G VPT AIG DAFQE
Sbjct: 80  HAADGYARATGEVGVALVTSGPGLTNAVTGIATAYMDSIPMVIISGQVPTPAIGLDAFQE 139

Query: 131 CDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYE-Y 189
           CDTVGITRPIVKHNFLVKD RDLAAT+KKAF IA TGRPGPVVVD+PKDVS     Y  Y
Sbjct: 140 CDTVGITRPIVKHNFLVKDPRDLAATMKKAFHIARTGRPGPVVVDVPKDVSFKKVPYTGY 199

Query: 190 PKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHP 249
           P+S++MRSYNPV KGH GQIRKA+ LL  A+RPYIYTGGGV+L NA++ELR L  + G+P
Sbjct: 200 PQSVEMRSYNPVRKGHGGQIRKALQLLLAAKRPYIYTGGGVLLGNATNELRTLVDMLGYP 259

Query: 250 VTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTS 309
           VTNTLMGLGA+P + ++F+GMLGMHGT EAN AMQNCDVL+A+GARFDDRVIGNP HF  
Sbjct: 260 VTNTLMGLGAYPASDRKFLGMLGMHGTIEANNAMQNCDVLLAVGARFDDRVIGNPKHFAQ 319

Query: 310 QARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIE 369
             RKIIH+DIDPSSISKRVKVDIPIVG+VKDVL ELI+ I+ S  +P   ALA WW+ IE
Sbjct: 320 NDRKIIHVDIDPSSISKRVKVDIPIVGDVKDVLTELISMIRESSTRPDAGALAAWWDTIE 379

Query: 370 QWRSVDCLKYDRSS-EIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQFYKFDEPRR 427
            WR  DCLKYD    ++IKPQYVVE +W +TK  D +I SDVGQHQMWAAQ+Y+FDEPRR
Sbjct: 380 GWRKRDCLKYDMGGPDVIKPQYVVETLWNMTKDADTYITSDVGQHQMWAAQYYRFDEPRR 439

Query: 428 WINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSL 487
           WINSGGLGTMGVG+PYAMGIK A P+ EV  ITGEGS+QM IQELSTCLQY+TP+KICSL
Sbjct: 440 WINSGGLGTMGVGIPYAMGIKLAKPQSEVFCITGEGSVQMNIQELSTCLQYNTPIKICSL 499

Query: 488 NNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFR 547
           NN YLGMVRQWQEIEY  RYSHSYMDALP+FVKLAEAYGHVG+ +E   DVEPALREA +
Sbjct: 500 NNRYLGMVRQWQEIEYSGRYSHSYMDALPNFVKLAEAYGHVGLLIEHPKDVEPALREARK 559

Query: 548 LKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           LKDRTVFLDF+TDPTENV+PMVQAGKGI+EMLLG+EDL
Sbjct: 560 LKDRTVFLDFRTDPTENVFPMVQAGKGITEMLLGSEDL 597


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: 1128
Number of extensions: 37
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: 585
Length of database: 597
Length adjustment: 37
Effective length of query: 548
Effective length of database: 560
Effective search space:   306880
Effective search space used:   306880
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 Ac3H11_525 (Acetolactate synthase large subunit (EC 2.2.1.6))
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.31533.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   7.6e-252  822.6   0.0   8.9e-252  822.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525  Acetolactate synthase large subu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525  Acetolactate synthase large subunit (EC 2.2.1.6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  822.4   0.0  8.9e-252  8.9e-252       2     554 ..      29     591 ..      28     594 .. 0.97

  Alignments for each domain:
  == domain 1  score: 822.4 bits;  conditional E-value: 8.9e-252
                                       TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGk 63 
                                                      g+eil++sl++e+v++++GyPGGavl iydaly ++ ++h+lvrheqaa+haadGyara+G+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525  29 MGSEILIKSLQAENVQYIWGYPGGAVLYIYDALYkQDTIQHVLVRHEQAAVHAADGYARATGE 91 
                                                     699*******************************9999************************* PP

                                       TIGR00118  64 vGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsf 126
                                                     vGv+l+tsGPG tn+vtgiatay+ds+P+v+++Gqv+t +iG dafqe+d +Git+p++kh+f
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525  92 VGVALVTSGPGLTNAVTGIATAYMDSIPMVIISGQVPTPAIGLDAFQECDTVGITRPIVKHNF 154
                                                     *************************************************************** PP

                                       TIGR00118 127 lvkkaedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghkl 188
                                                     lvk+++dl++++k+af+ia tGrPGPv+vd+Pkdv+ +++ ++ + ++ve+++y+p  kgh  
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525 155 LVKDPRDLAATMKKAFHIARTGRPGPVVVDVPKDVSFKKVPYTGYpQSVEMRSYNPVRKGHGG 217
                                                     **************************************99987555***************** PP

                                       TIGR00118 189 qikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgm 251
                                                     qi+kal+l+ +ak+P ++ GgGv+ ++a++el+ l+++l  pvt tl+GlGa+p+ ++++lgm
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525 218 QIRKALQLLLAAKRPYIYTGGGVLLGNATNELRTLVDMLGYPVTNTLMGLGAYPASDRKFLGM 280
                                                     *************************************************************** PP

                                       TIGR00118 252 lGmhGtkeanlavseadlliavGarfddrvtgnlakfapea.kiihididPaeigknvkvdip 313
                                                     lGmhGt ean a++++d+l+avGarfddrv gn ++fa++  kiih+didP++i+k vkvdip
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525 281 LGMHGTIEANNAMQNCDVLLAVGARFDDRVIGNPKHFAQNDrKIIHVDIDPSSISKRVKVDIP 343
                                                     **************************************98626******************** PP

                                       TIGR00118 314 ivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee.eesikPqkvikel 370
                                                     ivGd+k vl+el++ ++e     +      W++ ie w+k+ +lk+d    + ikPq+v+++l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525 344 IVGDVKDVLTELISMIRESstrpDAGALAaWWDTIEGWRKRDCLKYDMGgPDVIKPQYVVETL 406
                                                     ****************99965542333346***************99862678********** PP

                                       TIGR00118 371 skllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvv 432
                                                     ++++kd ++++t+dvGqhqmwaaq+y++++pr++i+sgGlGtmG G+P a+G+k+akp+++v 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525 407 WNMTKDaDTYITSDVGQHQMWAAQYYRFDEPRRWINSGGLGTMGVGIPYAMGIKLAKPQSEVF 469
                                                     *****999******************************************************* PP

                                       TIGR00118 433 avtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfv 495
                                                     ++tG+gs+qmn+qelst+ +y++p+ki+ lnn++lGmv+qWqe+ y++rys++++ + lp+fv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525 470 CITGEGSVQMNIQELSTCLQYNTPIKICSLNNRYLGMVRQWQEIEYSGRYSHSYMDA-LPNFV 531
                                                     ********************************************************5.***** PP

                                       TIGR00118 496 klaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554
                                                     klaeayG++g+ ie+p+++e +l+ea + k + v+ld++ d +e+v+Pmv  G+g++e++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_525 532 KLAEAYGHVGLLIEHPKDVEPALREARKLKdRTVFLDFRTDPTENVFPMVQAGKGITEML 591
                                                     **************************9987699*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (597 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: 00:00:00.07
# Mc/sec: 4.35
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis