GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Pontibacter ramchanderi LP43

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 WP_101445091.1 BD749_RS13350 biosynthetic-type acetolactate synthase large subunit

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_002846395.1:WP_101445091.1
          Length = 564

 Score =  462 bits (1189), Expect = e-134
 Identities = 254/561 (45%), Positives = 359/561 (63%), Gaps = 22/561 (3%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYA 58
           + GA+ V+ +L A+ V T+FGYPGGAIMPVYDALYD    + H+L RHEQGA  AA GYA
Sbjct: 5   VTGAEAVILSLLAENVETIFGYPGGAIMPVYDALYDYADQLNHILVRHEQGAIHAAQGYA 64

Query: 59  RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118
           R +GK GVC+ATSGPGATNLITGLADA  DS PVV ITGQV++  +GTDAFQE DV+ ++
Sbjct: 65  RVSGKVGVCLATSGPGATNLITGLADAKADSTPVVCITGQVASSLLGTDAFQEADVISIT 124

Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENE 178
            A TK +  V    ++P  +++AF +A SGRPGPVL+DI KD Q A     P+      +
Sbjct: 125 SAVTKWNLQVTQASDIPAAISKAFYLAQSGRPGPVLIDITKDAQFAK---TPFRYAPCKQ 181

Query: 179 VTF--PHAEVEQ-----ARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTL 231
           V +  P   ++Q     A  ++  ++KP++  G G+ +A A   L +      +P   TL
Sbjct: 182 VAYYAPKPPLDQQAVACAAALINSSRKPLILAGQGIHLAGAHQELLDLATKADIPVATTL 241

Query: 232 KGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVI 291
            GL A+  ++P  +G+LGMHG  A N    E DL+IAVG RFDDRVTG+++T+A  AS+I
Sbjct: 242 LGLSAIPTEHPLNVGLLGMHGNYAPNLKTNEADLIIAVGMRFDDRVTGRVDTYARQASII 301

Query: 292 HMDIDPAEMNKLRQAHVALQGDLNALLPALQQPL--NQY-DWQQH---CAQLRDEHSWRY 345
           H+D+DPAE+NK+ +A VAL  D    L AL + +  N++ +W Q    C     E   R+
Sbjct: 302 HIDLDPAEINKIIKADVALVADAREALAALTRLVFKNEHPEWLQEFRDCMDQEFEKVVRH 361

Query: 346 D-HPGD--AIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGT 402
           D  P D   I    +L+ +++    D V+ TDVGQHQM A+++       + ITS GLGT
Sbjct: 362 DLFPADDREITMGEVLRLVNELAEEDSVLVTDVGQHQMVASRYFNFRSLNSNITSGGLGT 421

Query: 403 MGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVR 462
           MGF LPAA+GA+  RP   VV + GDG F MN+QELGT+ +  + +K+++L+N  LGMVR
Sbjct: 422 MGFALPAAIGAKAGRPLAQVVAVIGDGGFQMNIQELGTIMQTGIAVKVIILNNNFLGMVR 481

Query: 463 QWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHV 522
           QWQQLFF++RYS   + +NPDF+ +   +GI  + + ++  +   +  +L+S  P +L V
Sbjct: 482 QWQQLFFEKRYSSVEM-ENPDFVKITQGYGISARKVVQRSALAETMRAVLSSQQPEVLEV 540

Query: 523 SIDELENVWPLVPPGASNSEM 543
            +   +NV+P++P GA  SE+
Sbjct: 541 VVGREDNVFPMIPTGACVSEV 561


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: 748
Number of extensions: 36
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: 564
Length adjustment: 36
Effective length of query: 512
Effective length of database: 528
Effective search space:   270336
Effective search space used:   270336
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 WP_101445091.1 BD749_RS13350 (biosynthetic-type 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.3425488.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-214  699.3   1.3     2e-214  699.1   1.3    1.0  1  NCBI__GCF_002846395.1:WP_101445091.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101445091.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  699.1   1.3    2e-214    2e-214       2     553 ..       6     561 ..       5     564 .] 0.97

  Alignments for each domain:
  == domain 1  score: 699.1 bits;  conditional E-value: 2e-214
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           +gae+++ sl +e+vet+fGyPGGa++p+ydaly  +++l+hilvrheq+a+haa+Gyar+sGkvGv+latsG
  NCBI__GCF_002846395.1:WP_101445091.1   6 TGAEAVILSLLAENVETIFGYPGGAIMPVYDALYdyADQLNHILVRHEQGAIHAAQGYARVSGKVGVCLATSG 78 
                                           79********************************989************************************ PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatnl+tg+a+a +ds+P+v +tGqva+sl+G+dafqe+d++ it +vtk++++v++a+d+p+ + +af++a
  NCBI__GCF_002846395.1:WP_101445091.1  79 PGATNLITGLADAKADSTPVVCITGQVASSLLGTDAFQEADVISITSAVTKWNLQVTQASDIPAAISKAFYLA 151
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218
                                           ++GrPGPvl+d+ kd + a++ +++    ++  y+p+   +++ ++ a+ li++++kP++l+G G+  a+a++
  NCBI__GCF_002846395.1:WP_101445091.1 152 QSGRPGPVLIDITKDAQFAKTPFRYAPCKQVAYYAPKPPLDQQAVACAAALINSSRKPLILAGQGIHLAGAHQ 224
                                           **************************9999999**************************************** PP

                             TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291
                                           el +la +++ipv+ttllGl a+p +hpl +g+lGmhG ++ nl  +eadl+iavG+rfddrvtg ++++a++
  NCBI__GCF_002846395.1:WP_101445091.1 225 ELLDLATKADIPVATTLLGLSAIPTEHPLNVGLLGMHGNYAPNLKTNEADLIIAVGMRFDDRVTGRVDTYARQ 297
                                           ************************************************************************* PP

                             TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilk......ldeee 358
                                           a iihid+dPaei+k++k+d+++v da++ l+ l + + ++e+ e  Wl++ ++  ++   k      +  ++
  NCBI__GCF_002846395.1:WP_101445091.1 298 ASIIHIDLDPAEINKIIKADVALVADAREALAALTRLVFKNEHPE--WLQEFRDCMDQEFEKvvrhdlFPADD 368
                                           ***************************************999888..99988766554443311112466788 PP

                             TIGR00118 359 esikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431
                                            +i   +v++ + +l+++++++ tdvGqhqm a++++++++ ++ itsgGlGtmGf lPaa+Gak + p ++v
  NCBI__GCF_002846395.1:WP_101445091.1 369 REITMGEVLRLVNELAEEDSVLVTDVGQHQMVASRYFNFRSLNSNITSGGLGTMGFALPAAIGAKAGRPLAQV 441
                                           99*********************************************************************** PP

                             TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504
                                           vav Gdg+fqmn+qel ti++ +i vk++ilnn++lGmv+qWq+lf+e+rys++++++  pdfvk++++yG+ 
  NCBI__GCF_002846395.1:WP_101445091.1 442 VAVIGDGGFQMNIQELGTIMQTGIAVKVIILNNNFLGMVRQWQQLFFEKRYSSVEMEN--PDFVKITQGYGIS 512
                                           ********************************************************97..************* PP

                             TIGR00118 505 giriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                           + ++ +++ l+e ++ +l+s++p +l+v+v +e++v+Pm+++Ga ++e+
  NCBI__GCF_002846395.1:WP_101445091.1 513 ARKVVQRSALAETMRAVLSSQQPEVLEVVVGREDNVFPMIPTGACVSEV 561
                                           *******************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (564 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: 16.98
//
[ok]

This GapMind analysis is from Jul 26 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:

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