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

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.4166516.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  FitnessBrowser__Pedo557:CA265_RS15805  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Pedo557:CA265_RS15805  
   #    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..dselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                            +g+++l++ l +egv t+fGyPGGa++piydaly  +++lehilvrheq+ +haa+G+arasG+vGvv+ats
  FitnessBrowser__Pedo557:CA265_RS15805  25 TGSQVLLNGLIEEGVTTIFGYPGGAIMPIYDALYdyADKLEHILVRHEQGGIHAAQGFARASGEVGVVFATS 96 
                                            6899******************************989*********************************** PP

                              TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafe 143
                                            GPGatnlvtg+a+a +ds+Plv +tGqv ++l+G+dafqe d++ it pvtk++++v++a+++ e+l +af+
  FitnessBrowser__Pedo557:CA265_RS15805  97 GPGATNLVTGLADAQIDSTPLVCITGQVFAHLLGTDAFQETDVINITTPVTKWNYQVTDAKEIQEVLAKAFY 168
                                            ************************************************************************ PP

                              TIGR00118 144 iastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvllvGgGviia 214
                                            ia++GrPGPvl+d+ k+ + +  e++ + +  ++++y+p+ k +   i++a+eli++akkP +l G Gvi +
  FitnessBrowser__Pedo557:CA265_RS15805 169 IAKSGRPGPVLIDITKNAQLQLEEFPEYvKCNHIRSYRPKPKVRIEYIEQAAELINSAKKPFVLFGQGVILG 240
                                            *******************99999987746678*************************************** PP

                              TIGR00118 215 easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnla 286
                                             a+ee+k + +++ ip + t++G Ga+p  hpl +gmlGmhG +  n+  +ead++ia+G+rfddrvtg l+
  FitnessBrowser__Pedo557:CA265_RS15805 241 SAEEEFKAFINKTGIPAAWTIMGEGAIPTSHPLNVGMLGMHGNYGPNVLTNEADVIIAIGMRFDDRVTGRLD 312
                                            ************************************************************************ PP

                              TIGR00118 287 kfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilk..... 353
                                            k+a++a+++h+didPaei+knvk+++ + Gd+k+ l  l + ++e+++++  Wl+k +++ +e i +     
  FitnessBrowser__Pedo557:CA265_RS15805 313 KYAKQARVVHLDIDPAEIDKNVKAEVGVWGDCKETLPLLTNLVNENKHED--WLAKFRQYNQEEIDQvitpe 382
                                            ************************************99888888877777..*********99887621111 PP

                              TIGR00118 354 ldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakva 425
                                            l  + +++   +v++++ ++  ++a++ tdvGqhqm a ++ k++++r+ itsgGlGtmGfGlPaa+Gak +
  FitnessBrowser__Pedo557:CA265_RS15805 383 LYPTGDEMTMGEVLRNINEICGGDAVIVTDVGQHQMVACRYAKFNNTRSNITSGGLGTMGFGLPAAIGAKYG 454
                                            33456789999************************************************************* PP

                              TIGR00118 426 kpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvkl 497
                                             p++tv+a+ Gdg+fqm+ qel ti++++  vki+ilnn++lGmv+qWq+lf+++rys ++++s  pdfv+l
  FitnessBrowser__Pedo557:CA265_RS15805 455 APDKTVIAIIGDGGFQMTPQELGTIMQFGAAVKILILNNRFLGMVRQWQQLFHDKRYSFVNITS--PDFVAL 524
                                            **************************************************************96..****** PP

                              TIGR00118 498 aeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                            a++y +++ ++ ++++l ++l+ ++++++ +ll+v v +e++v+Pmv++G++++e+
  FitnessBrowser__Pedo557:CA265_RS15805 525 AKSYYIEASKVDERANLRQALETMINHEGSYLLEVMVGRENNVFPMVPQGMSVSEI 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 21.69
//
[ok]

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

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