GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS15805 CA265_RS15805 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__Pedo557:CA265_RS15805
          Length = 583

 Score =  465 bits (1196), Expect = e-135
 Identities = 249/556 (44%), Positives = 348/556 (62%), Gaps = 16/556 (2%)

Query: 3   GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYARA 60
           G+Q +++ L  +GV T+FGYPGGAIMP+YDALYD    +EH+L RHEQG   AA G+ARA
Sbjct: 26  GSQVLLNGLIEEGVTTIFGYPGGAIMPIYDALYDYADKLEHILVRHEQGGIHAAQGFARA 85

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           +G+ GV  ATSGPGATNL+TGLADA +DS P+V ITGQV A  +GTDAFQE DV+ ++  
Sbjct: 86  SGEVGVVFATSGPGATNLVTGLADAQIDSTPLVCITGQVFAHLLGTDAFQETDVINITTP 145

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
            TK ++ V   +E+  ++A+AF +A SGRPGPVL+DI K+ QL   +   +         
Sbjct: 146 VTKWNYQVTDAKEIQEVLAKAFYIAKSGRPGPVLIDITKNAQLQLEEFPEYVKCNHIRSY 205

Query: 181 FPHAEV-----EQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLG 235
            P  +V     EQA +++  A+KP +  G GV +  A    + F+  T +PA  T+ G G
Sbjct: 206 RPKPKVRIEYIEQAAELINSAKKPFVLFGQGVILGSAEEEFKAFINKTGIPAAWTIMGEG 265

Query: 236 AVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDI 295
           A+   +P  +GMLGMHG    N    E D++IA+G RFDDRVTG+L+ +A  A V+H+DI
Sbjct: 266 AIPTSHPLNVGMLGMHGNYGPNVLTNEADVIIAIGMRFDDRVTGRLDKYAKQARVVHLDI 325

Query: 296 DPAEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDH-------- 347
           DPAE++K  +A V + GD    LP L   +N+   +   A+ R  +    D         
Sbjct: 326 DPAEIDKNVKAEVGVWGDCKETLPLLTNLVNENKHEDWLAKFRQYNQEEIDQVITPELYP 385

Query: 348 PGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGL 407
            GD +    +L+ +++    D V+ TDVGQHQM A ++       + ITS GLGTMGFGL
Sbjct: 386 TGDEMTMGEVLRNINEICGGDAVIVTDVGQHQMVACRYAKFNNTRSNITSGGLGTMGFGL 445

Query: 408 PAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQL 467
           PAA+GA+   P+ TV+ I GDG F M  QELGT+ +    +KI++L+N+ LGMVRQWQQL
Sbjct: 446 PAAIGAKYGAPDKTVIAIIGDGGFQMTPQELGTIMQFGAAVKILILNNRFLGMVRQWQQL 505

Query: 468 FFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDEL 527
           F  +RYS   +T +PDF+ LA ++ I    +  +  +  AL+TM+N +G YLL V +   
Sbjct: 506 FHDKRYSFVNIT-SPDFVALAKSYYIEASKVDERANLRQALETMINHEGSYLLEVMVGRE 564

Query: 528 ENVWPLVPPGASNSEM 543
            NV+P+VP G S SE+
Sbjct: 565 NNVFPMVPQGMSVSEI 580


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: 766
Number of extensions: 31
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: 583
Length adjustment: 36
Effective length of query: 512
Effective length of database: 547
Effective search space:   280064
Effective search space used:   280064
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 CA265_RS15805 CA265_RS15805 (acetolactate synthase, large subunit, biosynthetic type)
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.6482.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.5e-213  696.1   1.3   1.8e-213  695.9   1.3    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15805  CA265_RS15805 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15805  CA265_RS15805 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.9   1.3  1.8e-213  1.8e-213       2     553 ..      25     580 ..      24     583 .] 0.96

  Alignments for each domain:
  == domain 1  score: 695.9 bits;  conditional E-value: 1.8e-213
                                  TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvv 67 
                                                +g+++l++ l +egv t+fGyPGGa++piydaly  +++lehilvrheq+ +haa+G+arasG+vGvv
  lcl|FitnessBrowser__Pedo557:CA265_RS15805  25 TGSQVLLNGLIEEGVTTIFGYPGGAIMPIYDALYdyADKLEHILVRHEQGGIHAAQGFARASGEVGVV 92 
                                                6899******************************989******************************* PP

                                  TIGR00118  68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135
                                                +atsGPGatnlvtg+a+a +ds+Plv +tGqv ++l+G+dafqe d++ it pvtk++++v++a+++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS15805  93 FATSGPGATNLVTGLADAQIDSTPLVCITGQVFAHLLGTDAFQETDVINITTPVTKWNYQVTDAKEIQ 160
                                                ******************************************************************** PP

                                  TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakk 202
                                                e+l +af+ia++GrPGPvl+d+ k+ + +  e++ + +  ++++y+p+ k +   i++a+eli++akk
  lcl|FitnessBrowser__Pedo557:CA265_RS15805 161 EVLAKAFYIAKSGRPGPVLIDITKNAQLQLEEFPEYvKCNHIRSYRPKPKVRIEYIEQAAELINSAKK 228
                                                ***************************99999987746678*************************** PP

                                  TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadll 270
                                                P +l G Gvi + a+ee+k + +++ ip + t++G Ga+p  hpl +gmlGmhG +  n+  +ead++
  lcl|FitnessBrowser__Pedo557:CA265_RS15805 229 PFVLFGQGVILGSAEEEFKAFINKTGIPAAWTIMGEGAIPTSHPLNVGMLGMHGNYGPNVLTNEADVI 296
                                                ******************************************************************** PP

                                  TIGR00118 271 iavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke 338
                                                ia+G+rfddrvtg l+k+a++a+++h+didPaei+knvk+++ + Gd+k+ l  l + ++e+++++  
  lcl|FitnessBrowser__Pedo557:CA265_RS15805 297 IAIGMRFDDRVTGRLDKYAKQARVVHLDIDPAEIDKNVKAEVGVWGDCKETLPLLTNLVNENKHED-- 362
                                                ****************************************************99888888877777.. PP

                                  TIGR00118 339 Wlekieewkkeyilk.....ldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkpr 401
                                                Wl+k +++ +e i +     l  + +++   +v++++ ++  ++a++ tdvGqhqm a ++ k++++r
  lcl|FitnessBrowser__Pedo557:CA265_RS15805 363 WLAKFRQYNQEEIDQvitpeLYPTGDEMTMGEVLRNINEICGGDAVIVTDVGQHQMVACRYAKFNNTR 430
                                                *********9988762111133456789999************************************* PP

                                  TIGR00118 402 kfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGm 469
                                                + itsgGlGtmGfGlPaa+Gak + p++tv+a+ Gdg+fqm+ qel ti++++  vki+ilnn++lGm
  lcl|FitnessBrowser__Pedo557:CA265_RS15805 431 SNITSGGLGTMGFGLPAAIGAKYGAPDKTVIAIIGDGGFQMTPQELGTIMQFGAAVKILILNNRFLGM 498
                                                ******************************************************************** PP

                                  TIGR00118 470 vkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537
                                                v+qWq+lf+++rys ++++s  pdfv+la++y +++ ++ ++++l ++l+ ++++++ +ll+v v +e
  lcl|FitnessBrowser__Pedo557:CA265_RS15805 499 VRQWQQLFHDKRYSFVNITS--PDFVALAKSYYIEASKVDERANLRQALETMINHEGSYLLEVMVGRE 564
                                                ******************96..********************************************** PP

                                  TIGR00118 538 eevlPmvapGagldel 553
                                                ++v+Pmv++G++++e+
  lcl|FitnessBrowser__Pedo557:CA265_RS15805 565 NNVFPMVPQGMSVSEI 580
                                                ************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (583 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: 00:00:00.02
# Mc/sec: 11.47
//
[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