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 Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate BPHYT_RS10500 BPHYT_RS10500 acetolactate synthase

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__BFirm:BPHYT_RS10500
          Length = 600

 Score =  431 bits (1107), Expect = e-125
 Identities = 252/577 (43%), Positives = 343/577 (59%), Gaps = 37/577 (6%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEH----------LLCRHEQGA 50
           M+GA  ++  L  QGV+TVFGY GGAI+P YDA++     H          ++  +EQ A
Sbjct: 1   MSGADIILRVLSEQGVDTVFGYSGGAILPTYDAVFRFNEMHAQTPERQIKLVVPANEQAA 60

Query: 51  AMAAIGYARATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQ 110
              A GYARA+GK GV + TSGPGATN +T +AD   DSIPVV I GQV    IGTDAFQ
Sbjct: 61  GFMAAGYARASGKVGVFMVTSGPGATNAVTPIADCNGDSIPVVLICGQVPRAMIGTDAFQ 120

Query: 111 EVDVLGLSLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQ------LA 164
           E  V  +  AC K  FLV    +L + +  AF+VA +GRPGPV+VD+PKDIQ        
Sbjct: 121 EAPVFNIMSACAKQVFLVTDPAKLEQTLRTAFEVARTGRPGPVVVDVPKDIQNWTGTYQG 180

Query: 165 SGDLEPWFTTVENEVTFPHAEVEQARQ-----MLAKAQKPMLYVGGGVGMAQAVPALREF 219
            G LE    +    +    A +++ ++     +LA++++P+LY GGG+  A A   LR F
Sbjct: 181 QGTLEFRGYSDRLRMVAKGARLDEGKRNDFFGLLAQSKRPLLYAGGGIITAGATAELRRF 240

Query: 220 LAATKMPATCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTG 279
                +P   TL GLGA+   +   LGMLGMHG   AN+AV++CD LIAVGARFDDRV G
Sbjct: 241 AERFGIPVVTTLMGLGAISVRHELGLGMLGMHGAACANYAVEDCDFLIAVGARFDDRVAG 300

Query: 280 -KLNTFAPHAS-VIHMDIDPAEMNKLRQAHVALQGDLNALL-------PALQQPLNQYDW 330
            + + FAP A  V H+DID AE+NK+++AH A  GD    L       PA+Q  L   DW
Sbjct: 301 GRPDAFAPRARHVAHIDIDEAEINKVKRAHWAHVGDAKESLLSLMKHGPAVQPRL---DW 357

Query: 331 QQHCAQLRDEHSWRYDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTR 390
                +L+  +   YD    AI    ++++LS       +VTT VGQHQMWAAQ      
Sbjct: 358 LDRIKELKRVYGMNYDRNSPAIQPQFVVEKLSALTGGRAIVTTGVGQHQMWAAQFFDFVE 417

Query: 391 PENFITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKI 450
           P +F+TS  +GTMGFGLPAA+GAQ+ARP+  V+ I GDGS  MN+ +L T     +P+K+
Sbjct: 418 PRSFLTSGSMGTMGFGLPAAIGAQLARPDALVIDIDGDGSIRMNIGDLETATTYGVPVKV 477

Query: 451 VLLDNQRLGMVRQWQQLFFQER--YSETTLTDNPDFLMLASAFGIH-GQHITRKDQVEAA 507
           +LL+N   GM+RQWQ+LF++ R   S+ +L    DF+M A A G    + +   +++E  
Sbjct: 478 LLLNNLGDGMIRQWQRLFYEGRLCVSDKSL-HRKDFVMAAQADGFEFARRVATLNELEDQ 536

Query: 508 LDTMLNSDGPYLLHVSIDELENVWPLVPPGASNSEML 544
           L   +  DGP  L V +DE  +V+P+V PG S + M+
Sbjct: 537 LKAFIEFDGPAFLEVMVDENADVFPMVGPGQSYANMV 573


Lambda     K      H
   0.320    0.135    0.410 

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: 848
Number of extensions: 35
Number of successful extensions: 6
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: 548
Length of database: 600
Length adjustment: 36
Effective length of query: 512
Effective length of database: 564
Effective search space:   288768
Effective search space used:   288768
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_RS10500 BPHYT_RS10500 (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.10012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.8e-202  658.5   0.0   4.3e-202  658.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS10500  BPHYT_RS10500 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS10500  BPHYT_RS10500 acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  658.4   0.0  4.3e-202  4.3e-202       1     555 [.       1     574 [.       1     576 [. 0.95

  Alignments for each domain:
  == domain 1  score: 658.4 bits;  conditional E-value: 4.3e-202
                                TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..........dselehilvrheqaaahaadGyara 60 
                                              ++ga+i+++ l+++gv+tvfGy GGa+lp yda++          + +++ +++  eqaa  +a Gyara
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500   1 MSGADIILRVLSEQGVDTVFGYSGGAILPTYDAVFrfnemhaqtpERQIKLVVPANEQAAGFMAAGYARA 70 
                                              79*******************************9877666566555689********************* PP

                                TIGR00118  61 sGkvGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkk 130
                                              sGkvGv ++tsGPGatn+vt+ia+   ds+P+v++ Gqv++++iG+dafqe+ ++ i+ ++ k  flv++
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500  71 SGKVGVFMVTSGPGATNAVTPIADCNGDSIPVVLICGQVPRAMIGTDAFQEAPVFNIMSACAKQVFLVTD 140
                                              ********************************************************************** PP

                                TIGR00118 131 aedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptv....kghklq...ikka 193
                                              ++ l ++l+ afe+a tGrPGPv+vd+Pkd+++ + +++ + ++e++gy  ++    kg +l     +  
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500 141 PAKLEQTLRTAFEVARTGRPGPVVVDVPKDIQNWTGTYQGQGTLEFRGYSDRLrmvaKGARLDegkRNDF 210
                                              *************************************************766511113444334446677 PP

                                TIGR00118 194 leliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanla 263
                                                l++++k+P+l++GgG+i+a+a++el+++aer+ ipv+ttl+GlGa+   h+l lgmlGmhG++ an+a
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500 211 FGLLAQSKRPLLYAGGGIITAGATAELRRFAERFGIPVVTTLMGLGAISVRHELGLGMLGMHGAACANYA 280
                                              889******************************************************************* PP

                                TIGR00118 264 vseadlliavGarfddrvtg.nlakfapeak.iihididPaeigknvkvdipivGdakkvleellkklke 331
                                              v+++d liavGarfddrv+g   + fap+a+ + hidid aei+k+ +++ + vGdak+ l  l+k+  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500 281 VEDCDFLIAVGARFDDRVAGgRPDAFAPRARhVAHIDIDEAEINKVKRAHWAHVGDAKESLLSLMKHGPA 350
                                              ******************8626799*****8799*******************************99988 PP

                                TIGR00118 332 eekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkpr 401
                                              ++ +  +Wl++i+e+k+ y +++d+++ +i+Pq v+++ls l+ + aivtt+vGqhqmwaaqf+++ +pr
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500 351 VQPRL-DWLDRIKELKRVYGMNYDRNSPAIQPQFVVEKLSALTGGRAIVTTGVGQHQMWAAQFFDFVEPR 419
                                              87765.6*************************************************************** PP

                                TIGR00118 402 kfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvk 471
                                              +f+tsg +GtmGfGlPaa+Ga++a p++ v++++Gdgs+ mn+ +l+t++ y++pvk+++lnn   Gm++
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500 420 SFLTSGSMGTMGFGLPAAIGAQLARPDALVIDIDGDGSIRMNIGDLETATTYGVPVKVLLLNNLGDGMIR 489
                                              ********************************************************************** PP

                                TIGR00118 472 qWqelfyeerysetklaselpdfvklaeayGvk.giriekpeeleeklkealeskepvlldvevdkeeev 540
                                              qWq+lfye+r   +  + +  dfv  a+a G + + r+++ +ele++lk ++e ++p++l+v vd++++v
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500 490 QWQRLFYEGRLCVSDKSLHRKDFVMAAQADGFEfARRVATLNELEDQLKAFIEFDGPAFLEVMVDENADV 559
                                              ***********999999999***********975889********************************* PP

                                TIGR00118 541 lPmvapGagldelve 555
                                              +Pmv pG++ +++v+
  lcl|FitnessBrowser__BFirm:BPHYT_RS10500 560 FPMVGPGQSYANMVT 574
                                              ************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (600 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: 00:00:00.04
# Mc/sec: 7.74
//
[ok]

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

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Steps (tab-delimited)
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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