Alignments for a candidate for ilvI in Desulfovibrio vulgaris Hildenborough

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.1450.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.63
//
[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:

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