GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Klebsiella michiganensis M5al

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 BWI76_RS27815 BWI76_RS27815 acetolactate synthase catalytic subunit

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__Koxy:BWI76_RS27815
          Length = 562

 Score =  505 bits (1301), Expect = e-147
 Identities = 269/552 (48%), Positives = 359/552 (65%), Gaps = 16/552 (2%)

Query: 3   GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYARAT 61
           GAQ VVH L  QG+ TV G PGG+I+P+YDAL     + H+L RHEQGA   A G AR  
Sbjct: 15  GAQLVVHLLERQGITTVSGIPGGSILPIYDALSQSTQIRHILARHEQGAGFIAQGMARTE 74

Query: 62  GKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLAC 121
           GK  VC+A SGPGATNLIT +ADA LDSIP+V ITGQV A  IGTDAFQEVD  G+S+  
Sbjct: 75  GKPAVCMACSGPGATNLITAIADARLDSIPLVCITGQVPASMIGTDAFQEVDTYGISIPI 134

Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDL----EPWFTTVEN 177
           TKH++LV+++ ELP++M++AF +A SGRPGPV +DIPKD+Q A+ +L    EP       
Sbjct: 135 TKHNYLVRNIAELPQVMSDAFRIAQSGRPGPVWIDIPKDVQAATIELDALPEPGARMAAP 194

Query: 178 EVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237
           E  F  A V +A  M+  AQ+P+LY+GGGV    A   +R+      +P T TL  LG +
Sbjct: 195 E--FDSASVREAAAMINAAQRPVLYLGGGV--INAPEHIRQLAEKANLPTTQTLMALGML 250

Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297
              +P  LGMLGMHG ++ NF +QE DLL+ +GARFDDR  GK   F P+A +IH+DID 
Sbjct: 251 PKAHPLSLGMLGMHGARSTNFILQEADLLVVLGARFDDRAIGKTEQFCPNAKIIHVDIDR 310

Query: 298 AEMNKLRQAHVALQGD----LNALLPALQ-QPLNQYDWQQHCAQLRDEHSWRYDHPGDAI 352
           +E+ K++QAHVA+QGD    L  L+P ++ QP +   W Q  A L+ E         D +
Sbjct: 311 SELGKIKQAHVAIQGDVGEVLEQLIPQVEAQPRSA--WLQLVADLQREFPCTIPQEQDPL 368

Query: 353 YAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVG 412
               L+  ++     + +VTTDVGQHQMW AQ     RP  ++TS GLGTMGFGLPAAVG
Sbjct: 369 SHYGLINAVAACVDDEAIVTTDVGQHQMWVAQAYPLNRPRQWLTSGGLGTMGFGLPAAVG 428

Query: 413 AQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQER 472
           A +A P   V+C SGDGS MMN+QE+ T    QL +KI+L++N+ LG+V Q Q LF+++ 
Sbjct: 429 AALANPQRKVICFSGDGSLMMNIQEMATAAENQLDVKIILMNNEALGLVYQQQSLFYKQG 488

Query: 473 YSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWP 532
               T     +F+ +AS FG+    +  +   +AAL  +++  GP L+HV ID  E V+P
Sbjct: 489 VFAATYPGMVNFMQIASGFGLQTCDLNNEADPQAALQAIIDRPGPALIHVRIDAEEKVYP 548

Query: 533 LVPPGASNSEML 544
           +VPPGA+N+EM+
Sbjct: 549 MVPPGAANTEMV 560


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: 828
Number of extensions: 32
Number of successful extensions: 5
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: 562
Length adjustment: 36
Effective length of query: 512
Effective length of database: 526
Effective search space:   269312
Effective search space used:   269312
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 BWI76_RS27815 BWI76_RS27815 (acetolactate synthase catalytic 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.1326.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-205  669.8   0.8   1.6e-205  669.6   0.8    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27815  BWI76_RS27815 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27815  BWI76_RS27815 acetolactate synthase catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  669.6   0.8  1.6e-205  1.6e-205       2     555 ..      14     561 ..      13     562 .] 0.97

  Alignments for each domain:
  == domain 1  score: 669.6 bits;  conditional E-value: 1.6e-205
                               TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                             +ga+++v+ l+++g+ tv G+PGG++lpiydal  + +++hil+rheq+a  +a+G+ar+ Gk+ v++a s
  lcl|FitnessBrowser__Koxy:BWI76_RS27815  14 TGAQLVVHLLERQGITTVSGIPGGSILPIYDALSqSTQIRHILARHEQGAGFIAQGMARTEGKPAVCMACS 84 
                                             79*******************************97889********************************* PP

                               TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeaf 142
                                             GPGatnl+t+ia+a lds+Plv +tGqv++s+iG+dafqe+d  Gi++p+tkh++lv++ ++lp+++ +af
  lcl|FitnessBrowser__Koxy:BWI76_RS27815  85 GPGATNLITAIADARLDSIPLVCITGQVPASMIGTDAFQEVDTYGISIPITKHNYLVRNIAELPQVMSDAF 155
                                             *********************************************************************** PP

                               TIGR00118 143 eiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGvii 213
                                              ia++GrPGPv +d+Pkdv++a+iel+   +   +  +p+   + + +++a+ +i++a++Pvl+ GgGvi 
  lcl|FitnessBrowser__Koxy:BWI76_RS27815 156 RIAQSGRPGPVWIDIPKDVQAATIELDALPEPGARMAAPEF--DSASVREAAAMINAAQRPVLYLGGGVI- 223
                                             *************************9998776666666655..56789*********************9. PP

                               TIGR00118 214 aeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgn 284
                                              +a+e++++lae++++p t+tl+ lG +p+ hpl+lgmlGmhG++ +n+ ++eadll+ +Garfddr  g+
  lcl|FitnessBrowser__Koxy:BWI76_RS27815 224 -NAPEHIRQLAEKANLPTTQTLMALGMLPKAHPLSLGMLGMHGARSTNFILQEADLLVVLGARFDDRAIGK 293
                                             .57999***************************************************************** PP

                               TIGR00118 285 lakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkld 355
                                              ++f+p+akiih+did +e+gk+ +++++i Gd+ +vle+l+ +++++ ++   Wl+ ++++++e + ++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS27815 294 TEQFCPNAKIIHVDIDRSELGKIKQAHVAIQGDVGEVLEQLIPQVEAQPRSA--WLQLVADLQREFPCTIP 362
                                             **********************************************999998..***************** PP

                               TIGR00118 356 eeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvak 426
                                             +e++++    +i+++   ++deaivttdvGqhqmw+aq y+ ++pr+++tsgGlGtmGfGlPaa+Ga +a+
  lcl|FitnessBrowser__Koxy:BWI76_RS27815 363 QEQDPLSHYGLINAVAACVDDEAIVTTDVGQHQMWVAQAYPLNRPRQWLTSGGLGTMGFGLPAAVGAALAN 433
                                             *********************************************************************** PP

                               TIGR00118 427 peetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvkl 497
                                             p+ +v++ +Gdgs++mn+qe++t++e +++vki+++nne lG+v+q q+lfy++   +++   ++ +f+++
  lcl|FitnessBrowser__Koxy:BWI76_RS27815 434 PQRKVICFSGDGSLMMNIQEMATAAENQLDVKIILMNNEALGLVYQQQSLFYKQGVFAATYP-GMVNFMQI 503
                                             *****************************************************999888877.59****** PP

                               TIGR00118 498 aeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                             a ++G+++  ++++++ +++l+ ++   +p+l+ v++d ee+v+Pmv+pGa+++e+v+
  lcl|FitnessBrowser__Koxy:BWI76_RS27815 504 ASGFGLQTCDLNNEADPQAALQAIIDRPGPALIHVRIDAEEKVYPMVPPGAANTEMVG 561
                                             ********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (562 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: 8.21
//
[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:

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:

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:

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:

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