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.31783.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  lcl|FitnessBrowser__Burk376:H281DRAFT_00356  H281DRAFT_00356 acetolactate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00356  H281DRAFT_00356 acetolactate synthase, large subunit
   #    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..........dselehilvrheqaaahaadG 56 
                                                  ++ga+i+++ l ++gv+t+fGy GGa+lp yda++          + +++++++  eqaa  +a G
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356  22 MSGADIILRVLAEQGVDTLFGYSGGAILPTYDAVFrfneshaarpERQIKFVVPANEQAAGFMAAG 87 
                                                  79********************************98876656555568****************** PP

                                    TIGR00118  57 yarasGkvGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvt 122
                                                  yarasGkvGv ++tsGPGatn+vt+ia+   ds+P+v++ Gqv++++iGsdafqe+ ++ i+ ++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356  88 YARASGKVGVFMVTSGPGATNAVTPIADCNGDSIPVVLICGQVPRAAIGSDAFQEAPVFNIMSACA 153
                                                  ****************************************************************** PP

                                    TIGR00118 123 khsflvkkaedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykpt....vk 184
                                                  k  flv++++ l ++l+ afeia tGrPGPv+vd+Pkd+++   +++ + +++++gy  +     +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356 154 KQVFLVTDPAKLEQTLRTAFEIARTGRPGPVVVDVPKDIQNWVGQYQGQGTLHFRGYSDRlqlvAN 219
                                                  *********************************************************755111145 PP

                                    TIGR00118 185 ghklqikk...aleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhpl 247
                                                  g++l  +k     +l++++++P+l+vGgGvi+a+a++el+++aer +ipv+ttl+GlGa+p++hpl
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356 220 GSRLDEQKgaqFFDLLRQSERPLLYVGGGVIAAGATAELRQFAERYEIPVVTTLMGLGAIPAQHPL 285
                                                  666665551115679*************************************************** PP

                                    TIGR00118 248 algmlGmhGtkeanlavseadlliavGarfddrvtg.nlakfapeak.iihididPaeigknvkvd 311
                                                  +lgmlGmhG++ an+av+++d liavGarfddrv+g   ++fa+ a+ + hidid aei+k+ +++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356 286 SLGMLGMHGAACANYAVEDCDFLIAVGARFDDRVAGgRPDMFAAGARhVAHIDIDEAEINKVKRAH 351
                                                  **********************************8626799****98799**************** PP

                                    TIGR00118 312 ipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkde 377
                                                   + +Gda++ l+ l+++ +   ++   W+  ++e+++++ +++d+++  i+Pq+vi++ls+++ + 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356 352 WSHIGDARQALRALMEHESVALSSA-LWIGWVTELRQRHGMNYDRSNPLIQPQRVIEKLSEITGGR 416
                                                  ***************9877665554.6*************************************** PP

                                    TIGR00118 378 aivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmn 443
                                                  ai++t+vGqhqmw+aqfy++++pr+f+tsg +GtmGfGlPaa+Ga++a p++ v++++Gdgs+ mn
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356 417 AIISTGVGQHQMWTAQFYQFTEPRSFLTSGSMGTMGFGLPAAIGAQLARPDALVIDIDGDGSIRMN 482
                                                  ****************************************************************** PP

                                    TIGR00118 444 lqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk.giri 508
                                                    el+t++ y++pvk+++lnn+  Gm++qWq+lfye+r   +  a +  dfv  a+a G + + r+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356 483 AGELETASTYGVPVKVLLLNNRGDGMIRQWQRLFYEGRTFVSDKALHRKDFVMAARADGFEfACRV 548
                                                  **************************************9999888889***********87589** PP

                                    TIGR00118 509 ekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                                  e+p+el+eklk +++ ++p++l+v +d++++v+Pmv pG++ +++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00356 549 ETPSELDEKLKAFVAFEGPAFLEVMIDQNADVFPMVGPGQSYSNMIT 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.36
//
[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