Alignments for a candidate for ilvI in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_00356 H281DRAFT_00356 acetolactate synthase, large subunit

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__Burk376:H281DRAFT_00356
          Length = 621

 Score =  429 bits (1102), Expect = e-124
 Identities = 246/573 (42%), Positives = 336/573 (58%), Gaps = 29/573 (5%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEH----------LLCRHEQGA 50
           M+GA  ++  L  QGV+T+FGY GGAI+P YDA++     H          ++  +EQ A
Sbjct: 22  MSGADIILRVLAEQGVDTLFGYSGGAILPTYDAVFRFNESHAARPERQIKFVVPANEQAA 81

Query: 51  AMAAIGYARATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQ 110
              A GYARA+GK GV + TSGPGATN +T +AD   DSIPVV I GQV    IG+DAFQ
Sbjct: 82  GFMAAGYARASGKVGVFMVTSGPGATNAVTPIADCNGDSIPVVLICGQVPRAAIGSDAFQ 141

Query: 111 EVDVLGLSLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEP 170
           E  V  +  AC K  FLV    +L + +  AF++A +GRPGPV+VD+PKDIQ   G  + 
Sbjct: 142 EAPVFNIMSACAKQVFLVTDPAKLEQTLRTAFEIARTGRPGPVVVDVPKDIQNWVGQYQG 201

Query: 171 WFTT-----------VENEVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREF 219
             T            V N       +  Q   +L ++++P+LYVGGGV  A A   LR+F
Sbjct: 202 QGTLHFRGYSDRLQLVANGSRLDEQKGAQFFDLLRQSERPLLYVGGGVIAAGATAELRQF 261

Query: 220 LAATKMPATCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTG 279
               ++P   TL GLGA+ A +P  LGMLGMHG   AN+AV++CD LIAVGARFDDRV G
Sbjct: 262 AERYEIPVVTTLMGLGAIPAQHPLSLGMLGMHGAACANYAVEDCDFLIAVGARFDDRVAG 321

Query: 280 -KLNTFAPHAS-VIHMDIDPAEMNKLRQAHVALQGDLNALLPALQQ----PLNQYDWQQH 333
            + + FA  A  V H+DID AE+NK+++AH +  GD    L AL +     L+   W   
Sbjct: 322 GRPDMFAAGARHVAHIDIDEAEINKVKRAHWSHIGDARQALRALMEHESVALSSALWIGW 381

Query: 334 CAQLRDEHSWRYDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPEN 393
             +LR  H   YD     I    ++++LS+      +++T VGQHQMW AQ    T P +
Sbjct: 382 VTELRQRHGMNYDRSNPLIQPQRVIEKLSEITGGRAIISTGVGQHQMWTAQFYQFTEPRS 441

Query: 394 FITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLL 453
           F+TS  +GTMGFGLPAA+GAQ+ARP+  V+ I GDGS  MN  EL T     +P+K++LL
Sbjct: 442 FLTSGSMGTMGFGLPAAIGAQLARPDALVIDIDGDGSIRMNAGELETASTYGVPVKVLLL 501

Query: 454 DNQRLGMVRQWQQLFFQER-YSETTLTDNPDFLMLASAFGIH-GQHITRKDQVEAALDTM 511
           +N+  GM+RQWQ+LF++ R +         DF+M A A G      +    +++  L   
Sbjct: 502 NNRGDGMIRQWQRLFYEGRTFVSDKALHRKDFVMAARADGFEFACRVETPSELDEKLKAF 561

Query: 512 LNSDGPYLLHVSIDELENVWPLVPPGASNSEML 544
           +  +GP  L V ID+  +V+P+V PG S S M+
Sbjct: 562 VAFEGPAFLEVMIDQNADVFPMVGPGQSYSNMI 594


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: 884
Number of extensions: 50
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: 621
Length adjustment: 36
Effective length of query: 512
Effective length of database: 585
Effective search space:   299520
Effective search space used:   299520
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 H281DRAFT_00356 H281DRAFT_00356 (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.2135235.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.4e-204  666.6   0.0   1.6e-204  666.4   0.0    1.0  1  FitnessBrowser__Burk376:H281DRAFT_00356  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Burk376:H281DRAFT_00356  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.4   0.0  1.6e-204  1.6e-204       1     555 [.      22     595 ..      22     597 .. 0.95

  Alignments for each domain:
  == domain 1  score: 666.4 bits;  conditional E-value: 1.6e-204
                                TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..........dselehilvrheqaaahaadGyara 60 
                                              ++ga+i+++ l ++gv+t+fGy GGa+lp yda++          + +++++++  eqaa  +a Gyara
  FitnessBrowser__Burk376:H281DRAFT_00356  22 MSGADIILRVLAEQGVDTLFGYSGGAILPTYDAVFrfneshaarpERQIKFVVPANEQAAGFMAAGYARA 91 
                                              79********************************98876656555568********************** PP

                                TIGR00118  61 sGkvGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkk 130
                                              sGkvGv ++tsGPGatn+vt+ia+   ds+P+v++ Gqv++++iGsdafqe+ ++ i+ ++ k  flv++
  FitnessBrowser__Burk376:H281DRAFT_00356  92 SGKVGVFMVTSGPGATNAVTPIADCNGDSIPVVLICGQVPRAAIGSDAFQEAPVFNIMSACAKQVFLVTD 161
                                              ********************************************************************** PP

                                TIGR00118 131 aedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykpt....vkghklqikk...a 193
                                              ++ l ++l+ afeia tGrPGPv+vd+Pkd+++   +++ + +++++gy  +     +g++l  +k    
  FitnessBrowser__Burk376:H281DRAFT_00356 162 PAKLEQTLRTAFEIARTGRPGPVVVDVPKDIQNWVGQYQGQGTLHFRGYSDRlqlvANGSRLDEQKgaqF 231
                                              *************************************************755111145666665551115 PP

                                TIGR00118 194 leliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanla 263
                                               +l++++++P+l+vGgGvi+a+a++el+++aer +ipv+ttl+GlGa+p++hpl+lgmlGmhG++ an+a
  FitnessBrowser__Burk376:H281DRAFT_00356 232 FDLLRQSERPLLYVGGGVIAAGATAELRQFAERYEIPVVTTLMGLGAIPAQHPLSLGMLGMHGAACANYA 301
                                              679******************************************************************* PP

                                TIGR00118 264 vseadlliavGarfddrvtg.nlakfapeak.iihididPaeigknvkvdipivGdakkvleellkklke 331
                                              v+++d liavGarfddrv+g   ++fa+ a+ + hidid aei+k+ +++ + +Gda++ l+ l+++ + 
  FitnessBrowser__Burk376:H281DRAFT_00356 302 VEDCDFLIAVGARFDDRVAGgRPDMFAAGARhVAHIDIDEAEINKVKRAHWSHIGDARQALRALMEHESV 371
                                              ******************8626799****98799*******************************98776 PP

                                TIGR00118 332 eekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkpr 401
                                                ++   W+  ++e+++++ +++d+++  i+Pq+vi++ls+++ + ai++t+vGqhqmw+aqfy++++pr
  FitnessBrowser__Burk376:H281DRAFT_00356 372 ALSSA-LWIGWVTELRQRHGMNYDRSNPLIQPQRVIEKLSEITGGRAIISTGVGQHQMWTAQFYQFTEPR 440
                                              65554.6*************************************************************** PP

                                TIGR00118 402 kfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvk 471
                                              +f+tsg +GtmGfGlPaa+Ga++a p++ v++++Gdgs+ mn  el+t++ y++pvk+++lnn+  Gm++
  FitnessBrowser__Burk376:H281DRAFT_00356 441 SFLTSGSMGTMGFGLPAAIGAQLARPDALVIDIDGDGSIRMNAGELETASTYGVPVKVLLLNNRGDGMIR 510
                                              ********************************************************************** PP

                                TIGR00118 472 qWqelfyeerysetklaselpdfvklaeayGvk.giriekpeeleeklkealeskepvlldvevdkeeev 540
                                              qWq+lfye+r   +  a +  dfv  a+a G + + r+e+p+el+eklk +++ ++p++l+v +d++++v
  FitnessBrowser__Burk376:H281DRAFT_00356 511 QWQRLFYEGRTFVSDKALHRKDFVMAARADGFEfACRVETPSELDEKLKAFVAFEGPAFLEVMIDQNADV 580
                                              **********9999888889***********87589********************************** PP

                                TIGR00118 541 lPmvapGagldelve 555
                                              +Pmv pG++ +++++
  FitnessBrowser__Burk376:H281DRAFT_00356 581 FPMVGPGQSYSNMIT 595
                                              ************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (621 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: 30.18
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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