GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Desulfovibrio vulgaris Hildenborough

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate 206818 DVU1376 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-18810
         (585 letters)



>MicrobesOnline__882:206818
          Length = 563

 Score =  608 bits (1568), Expect = e-178
 Identities = 313/565 (55%), Positives = 401/565 (70%), Gaps = 6/565 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GA+IL+  L +EGV+  +GYPGGAV+ IYDE+ +  +  H+LVRHEQAAVHAADGYA
Sbjct: 2   QLNGAQILLECLKKEGVDVFFGYPGGAVIDIYDEIPRHPELHHVLVRHEQAAVHAADGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RA+GKVGV LVTSGPG TN VTGIATAY DSIP+V++TG VPT  IG DAFQE D VGIT
Sbjct: 62  RASGKVGVCLVTSGPGATNTVTGIATAYSDSIPVVILTGQVPTPLIGNDAFQEVDIVGIT 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LV+DV++LA  +++AF++A TGRPGPV+VD+PKDV +    + +P+ + MRS
Sbjct: 122 RPCTKHNYLVRDVKELATVVRQAFYLARTGRPGPVLVDLPKDVMQAKTDFVWPEDVSMRS 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  K +  QIR+A      AERP ++ GGGVV+++AS+EL   A     PV +TLMGL
Sbjct: 182 YNPTYKPNLNQIRRAADAFFEAERPLLFVGGGVVMSDASEELGWFARTLRIPVASTLMGL 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG    ++GMLGMHGTY AN A+ N D+++A+GARFDDRV G  + F S+AR IIHI
Sbjct: 242 GAFPGDDPLWLGMLGMHGTYAANKAVNNADLIVAVGARFDDRVTGRLSAFASKAR-IIHI 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPK--REALAKWWEQIEQWRSVD 375
           DIDP+SI K V+V IP+VG+ +  L   I +I    ++ K    A A+W EQ+  WR   
Sbjct: 301 DIDPTSIRKNVQVGIPVVGDCRQSLAN-IREILVPRLEEKDWGAAHARWLEQLASWRVEQ 359

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
            L + R    IKPQ V+E+++ +T+GDA I ++VGQ+QMW AQFY F +PR  I SGGLG
Sbjct: 360 PLGFSREGG-IKPQQVIEQLFAITRGDAIITTEVGQNQMWTAQFYTFRKPRTLITSGGLG 418

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG G P A+G + AFP+K VV + G+GSIQM IQEL+T +    PVKI  LNNGYLGMV
Sbjct: 419 TMGYGFPAAIGAQFAFPDKLVVDVAGDGSIQMNIQELATAVCNKLPVKILILNNGYLGMV 478

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE+ Y   Y  + MDA PDFVKLAEAYG  G R+ +   +E  LREA         +
Sbjct: 479 RQWQELFYQRNYCSTCMDAQPDFVKLAEAYGAEGYRITEVESLESTLREAL-ASPHPAII 537

Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580
           D + +  ENV+PMV AG  + EMLL
Sbjct: 538 DVRVEREENVYPMVPAGAALDEMLL 562


Lambda     K      H
   0.319    0.135    0.407 

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: 896
Number of extensions: 29
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: 585
Length of database: 563
Length adjustment: 36
Effective length of query: 549
Effective length of database: 527
Effective search space:   289323
Effective search space used:   289323
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 206818 DVU1376 (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.30474.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-257  841.7   0.0   1.4e-257  841.5   0.0    1.0  1  lcl|MicrobesOnline__882:206818  DVU1376 acetolactate synthase, l


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206818  DVU1376 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  841.5   0.0  1.4e-257  1.4e-257       1     554 [.       3     561 ..       3     563 .] 0.97

  Alignments for each domain:
  == domain 1  score: 841.5 bits;  conditional E-value: 1.4e-257
                       TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 
                                     l+ga+il+e lkkegv++ fGyPGGav++iyd++  + el+h+lvrheqaa+haadGyarasGkvGv+l+tsGPGatn+
  lcl|MicrobesOnline__882:206818   3 LNGAQILLECLKKEGVDVFFGYPGGAVIDIYDEIPrHPELHHVLVRHEQAAVHAADGYARASGKVGVCLVTSGPGATNT 81 
                                     579*******************************9899***************************************** PP

                       TIGR00118  79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdl 157
                                     vtgiatay ds+P+v+ltGqv+t liG+dafqe+di+Git+p+tkh++lv+++++l++++++af++a tGrPGPvlvdl
  lcl|MicrobesOnline__882:206818  82 VTGIATAYSDSIPVVILTGQVPTPLIGNDAFQEVDIVGITRPCTKHNYLVRDVKELATVVRQAFYLARTGRPGPVLVDL 160
                                     ******************************************************************************* PP

                       TIGR00118 158 PkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttll 236
                                     Pkdv++a++++  +e+v++++y+pt k++ +qi++a+++  +a++P+l+vGgGv++++aseel  +a +l+ipv++tl+
  lcl|MicrobesOnline__882:206818 161 PKDVMQAKTDFVWPEDVSMRSYNPTYKPNLNQIRRAADAFFEAERPLLFVGGGVVMSDASEELGWFARTLRIPVASTLM 239
                                     ******************************************************************************* PP

                       TIGR00118 237 GlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipiv 315
                                     GlGafp d+pl lgmlGmhGt++an av++adl++avGarfddrvtg l+ fa++a+iihididP++i knv+v ip+v
  lcl|MicrobesOnline__882:206818 240 GLGAFPGDDPLWLGMLGMHGTYAANKAVNNADLIVAVGARFDDRVTGRLSAFASKARIIHIDIDPTSIRKNVQVGIPVV 318
                                     ******************************************************************************* PP

                       TIGR00118 316 Gdakkvleellkklkee......ekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhq 388
                                     Gd+++ l+++ + l  +         + +Wle++++w+ e++l +++ e+ ikPq+vi++l  +++++ai+tt+vGq+q
  lcl|MicrobesOnline__882:206818 319 GDCRQSLANIREILVPRleekdwGAAHARWLEQLASWRVEQPLGFSR-EGGIKPQQVIEQLFAITRGDAIITTEVGQNQ 396
                                     *******9987766555433355445567*************99975.689**************************** PP

                       TIGR00118 389 mwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnell 467
                                     mw+aqfy+++kpr+ itsgGlGtmG+G+Paa+Ga+ a p++ vv+v+Gdgs+qmn+qel+t+v  ++pvki+ilnn +l
  lcl|MicrobesOnline__882:206818 397 MWTAQFYTFRKPRTLITSGGLGTMGYGFPAAIGAQFAFPDKLVVDVAGDGSIQMNIQELATAVCNKLPVKILILNNGYL 475
                                     ******************************************************************************* PP

                       TIGR00118 468 GmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546
                                     Gmv+qWqelfy++ y +t++ + +pdfvklaeayG++g ri++ e le+ l+eal+s +p+++dv+v++ee+v+Pmv+ 
  lcl|MicrobesOnline__882:206818 476 GMVRQWQELFYQRNYCSTCMDA-QPDFVKLAEAYGAEGYRITEVESLESTLREALASPHPAIIDVRVEREENVYPMVPA 553
                                     *********************5.******************************************************** PP

                       TIGR00118 547 Gagldelv 554
                                     Ga+lde++
  lcl|MicrobesOnline__882:206818 554 GAALDEML 561
                                     *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (563 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: 00:00:00.04
# Mc/sec: 6.93
//
[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