Alignments for a candidate for ilvI in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Burkholderia phytofirmans PsJN

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate BPHYT_RS06545 BPHYT_RS06545 acetolactate synthase

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



>FitnessBrowser__BFirm:BPHYT_RS06545
          Length = 587

 Score =  953 bits (2464), Expect = 0.0
 Identities = 458/585 (78%), Positives = 523/585 (89%)

Query: 1   MPSAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEH 60
           MPSAEFS +D+      + IGA +L+ ALA+E VE+VWGYPGG+VLYIYDEL+KQ KF+H
Sbjct: 3   MPSAEFSTSDTTPHPEADSIGATVLMKALADEDVEFVWGYPGGSVLYIYDELYKQDKFQH 62

Query: 61  ILVRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPT 120
           ILVRHEQAAVHAAD Y+R+TGKVGV LVTSGPGVTNAVTGIATAY+DSIPMVVI+G VPT
Sbjct: 63  ILVRHEQAAVHAADAYSRSTGKVGVCLVTSGPGVTNAVTGIATAYMDSIPMVVISGQVPT 122

Query: 121 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV 180
            AIGQDAFQECDTVGITRP VKHNFLVKDVRDLAAT+KKAFFIA TGRPGPV++DIPKDV
Sbjct: 123 AAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVKKAFFIARTGRPGPVLIDIPKDV 182

Query: 181 SRNACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELR 240
           S+  C+YE  K++ +RSYNPV KGHSGQIRKAV+LL  A+RPYIYTGGG++LA+AS EL 
Sbjct: 183 SKAPCQYEPLKTVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTGGGIILADASRELN 242

Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300
           Q A L G+PVTNTLMGLG +  + K+F+GMLGMHGTYEANMAMQ+CDVLIAIGARFDDRV
Sbjct: 243 QFADLLGYPVTNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARFDDRV 302

Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360
           IG+PAHF+S+ RKIIHIDIDPSSISKRVKVDIPIVG+VK+VL+ELI Q++ ++  P   A
Sbjct: 303 IGDPAHFSSRPRKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAEHGPDTAA 362

Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFY 420
           LA WW+ IE WR+ DCLK+DR S+IIKPQYVVEK WELT G+AF+CSDVGQHQMWAAQFY
Sbjct: 363 LADWWKDIEAWRAKDCLKFDRKSDIIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFY 422

Query: 421 KFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDT 480
           +F++PRRWINSGGLGTMG GLP AMG+K A P+ +V+ ITGEGSIQMCIQELSTC QY+T
Sbjct: 423 RFNKPRRWINSGGLGTMGFGLPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYET 482

Query: 481 PVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEP 540
           PVKI SLNN YLGMVRQWQ+IEY  RYSHSYMDALPDFVKLAEAYGHVGMR+E+T+DVEP
Sbjct: 483 PVKIISLNNRYLGMVRQWQQIEYSKRYSHSYMDALPDFVKLAEAYGHVGMRIERTADVEP 542

Query: 541 ALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           AL+EA RLKDRTVFLDFQTDPTENVWPMVQAGKGI+EML+G+EDL
Sbjct: 543 ALKEALRLKDRTVFLDFQTDPTENVWPMVQAGKGITEMLMGSEDL 587


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: 1061
Number of extensions: 25
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: 585
Length of database: 587
Length adjustment: 37
Effective length of query: 548
Effective length of database: 550
Effective search space:   301400
Effective search space used:   301400
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 BPHYT_RS06545 BPHYT_RS06545 (acetolactate synthase)
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.30178.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   5.6e-261  852.8   0.0   6.5e-261  852.5   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS06545  BPHYT_RS06545 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS06545  BPHYT_RS06545 acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  852.5   0.0  6.5e-261  6.5e-261       3     554 ..      23     581 ..      21     584 .. 0.98

  Alignments for each domain:
  == domain 1  score: 852.5 bits;  conditional E-value: 6.5e-261
                                TIGR00118   3 gaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                              ga++l+++l +e+ve v+GyPGG+vl iyd+ly +++++hilvrheqaa+haad y+r++GkvGv+l+ts
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545  23 GATVLMKALADEDVEFVWGYPGGSVLYIYDELYkQDKFQHILVRHEQAAVHAADAYSRSTGKVGVCLVTS 92 
                                              899******************************999********************************** PP

                                TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkea 141
                                              GPG tn+vtgiatay+ds+P+vv++Gqv+t++iG+dafqe+d +Git+p++kh+flvk+++dl++++k+a
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545  93 GPGVTNAVTGIATAYMDSIPMVVISGQVPTAAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVKKA 162
                                              ********************************************************************** PP

                                TIGR00118 142 feiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGv 211
                                              f ia tGrPGPvl+d+Pkdv++a +++e  ++v+l++y+p +kgh  qi+ka+ l+ +ak+P ++ GgG+
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545 163 FFIARTGRPGPVLIDIPKDVSKAPCQYEPLKTVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTGGGI 232
                                              ********************************************************************** PP

                                TIGR00118 212 iiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrv 281
                                              i a+as+el+++a+ l  pvt tl+GlG++ + ++++lgmlGmhGt+ean+a++++d+lia+Garfddrv
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545 233 ILADASRELNQFADLLGYPVTNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARFDDRV 302
                                              ********************************************************************** PP

                                TIGR00118 282 tgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekiee 345
                                               g+ a+f+++  kiihididP++i+k vkvdipivGd+k+vl+el+++l++     ++     W++ ie 
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545 303 IGDPAHFSSRPrKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAehgpDTAALAdWWKDIEA 372
                                              *******998627***********************************999866653333335******* PP

                                TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfG 415
                                              w+++ +lk+d++++ ikPq+v+++ ++l++++a+v +dvGqhqmwaaqfy+++kpr++i+sgGlGtmGfG
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545 373 WRAKDCLKFDRKSDIIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFYRFNKPRRWINSGGLGTMGFG 442
                                              ********************************************************************** PP

                                TIGR00118 416 lPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeeryset 485
                                              lPaa+G+k+a+p+++v+++tG+gs+qm +qelst+++y++pvki+ lnn++lGmv+qWq++ y++rys++
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545 443 LPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYETPVKIISLNNRYLGMVRQWQQIEYSKRYSHS 512
                                              ********************************************************************** PP

                                TIGR00118 486 klaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554
                                              ++ + lpdfvklaeayG++g+rie+ +++e +lkeal+ k + v+ld++ d +e+v+Pmv  G+g++e++
  lcl|FitnessBrowser__BFirm:BPHYT_RS06545 513 YMDA-LPDFVKLAEAYGHVGMRIERTADVEPALKEALRLKdRTVFLDFQTDPTENVWPMVQAGKGITEML 581
                                              ***5.********************************988689*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (587 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.10
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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