Alignments for a candidate for ilvI in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfovibrio gracilis DSM 16080

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_078716927.1 B5D49_RS06785 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900167125.1:WP_078716927.1
          Length = 564

 Score =  643 bits (1659), Expect = 0.0
 Identities = 327/565 (57%), Positives = 412/565 (72%), Gaps = 5/565 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GA++L+  L +E V+ V+G+PGGAV+ IYDEL      EHILVRHEQ A+HAADGYA
Sbjct: 2   ELTGAQVLLKCLEKENVKTVFGFPGGAVIDIYDEL-PNFPMEHILVRHEQGAIHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATG+VGV LVTSGPG TNAVTGIATAY+DSIP+V+ TG VPT  IG DAFQE D VGIT
Sbjct: 61  RATGEVGVCLVTSGPGATNAVTGIATAYMDSIPVVIFTGQVPTPLIGNDAFQEVDIVGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKDV+DLA  +K+AF++A +GRPGPV+VD+PKDV +  C +EYP+++ MRS
Sbjct: 121 RPCTKHNYLVKDVKDLARVVKQAFYLARSGRPGPVLVDLPKDVMQATCGFEYPRNVRMRS 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  + HS Q +K   LLQ AERP IY+GGGV+ A A  EL  LA     PVT+TLMGL
Sbjct: 181 YNPNLRPHSRQTKKVAKLLQEAERPLIYSGGGVISAQAHRELTWLARRLNIPVTSTLMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG  + ++GMLGMHGTY ANMA+ +CD+++AIGARFDDRV G    F  +A  I+H+
Sbjct: 241 GAFPGDDELWLGMLGMHGTYAANMAVNHCDLMLAIGARFDDRVTGKINTFAPEA-TIVHV 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKAS-DIKPKREALAKWWEQIEQWRSVDC 376
           DIDP+SI K V V +P+V + K  L  L  +++   D+       A W +++  W     
Sbjct: 300 DIDPTSIQKNVAVHVPLVADCKSALSSLKEEMEPGLDVAAWTAKHAGWVDRVRSWAKEHP 359

Query: 377 LKYDRS-SEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           L Y  S +  IKPQ+VVEKI+E+TKGDA + ++VGQ+QMWAAQFY+F  P  +++SGGLG
Sbjct: 360 LTYAPSETGAIKPQFVVEKIYEITKGDAIVATEVGQNQMWAAQFYRFKSPNSFLSSGGLG 419

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG G P A+G +KAFP+K VV I G+GSIQMCIQE++T +  D PVKI  LNNGYLGMV
Sbjct: 420 TMGYGFPAALGAQKAFPDKLVVNIAGDGSIQMCIQEMATAVCNDLPVKIVILNNGYLGMV 479

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE+ Y   Y  + MDA PDFVKLAEAYG  G RV ++ DVE  LR+AF    +   +
Sbjct: 480 RQWQELFYRKNYCQTCMDAQPDFVKLAEAYGAEGYRVTESGDVESVLRQAFS-SSKPAIV 538

Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580
           D + +  ENV+PMV AG  I+EMLL
Sbjct: 539 DVRVEKEENVYPMVPAGASITEMLL 563


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: 905
Number of extensions: 32
Number of successful extensions: 4
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: 564
Length adjustment: 36
Effective length of query: 549
Effective length of database: 528
Effective search space:   289872
Effective search space used:   289872
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_078716927.1 B5D49_RS06785 (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.20800.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-258  844.8   0.0   1.6e-258  844.6   0.0    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078716927.1  B5D49_RS06785 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078716927.1  B5D49_RS06785 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  844.6   0.0  1.6e-258  1.6e-258       1     554 [.       3     562 ..       3     564 .] 0.98

  Alignments for each domain:
  == domain 1  score: 844.6 bits;  conditional E-value: 1.6e-258
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+ga++l++ l+ke+v+tvfG+PGGav++iyd+l +  +ehilvrheq+a+haadGyara+G+vGv+l+
  lcl|NCBI__GCF_900167125.1:WP_078716927.1   3 LTGAQVLLKCLEKENVKTVFGFPGGAVIDIYDELPNFPMEHILVRHEQGAIHAADGYARATGEVGVCLV 71 
                                               68******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgiatay+ds+P+v++tGqv+t liG+dafqe+di+Git+p+tkh++lvk+++dl++++
  lcl|NCBI__GCF_900167125.1:WP_078716927.1  72 TSGPGATNAVTGIATAYMDSIPVVIFTGQVPTPLIGNDAFQEVDIVGITRPCTKHNYLVKDVKDLARVV 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k+af++a +GrPGPvlvdlPkdv++a++ +e++++v +++y+p++++h +q kk+++l+++a++P+++ 
  lcl|NCBI__GCF_900167125.1:WP_078716927.1 141 KQAFYLARSGRPGPVLVDLPKDVMQATCGFEYPRNVRMRSYNPNLRPHSRQTKKVAKLLQEAERPLIYS 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi a+a++el+ la rl+ipvt+tl+GlGafp d++l lgmlGmhGt++an+av+++dl++a+Gar
  lcl|NCBI__GCF_900167125.1:WP_078716927.1 210 GGGVISAQAHRELTWLARRLNIPVTSTLMGLGAFPGDDELWLGMLGMHGTYAANMAVNHCDLMLAIGAR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee......ekkekeW 339
                                               fddrvtg++++fapea+i+h+didP++i+knv+v++p+v d+k+ l+ l ++++        + k+  W
  lcl|NCBI__GCF_900167125.1:WP_078716927.1 279 FDDRVTGKINTFAPEATIVHVDIDPTSIQKNVAVHVPLVADCKSALSSLKEEMEPGldvaawTAKHAGW 347
                                               ***************************************************99987777776566666* PP

                                 TIGR00118 340 lekieewkkeyilk.ldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               ++++++w ke++l+   +e ++ikPq v++++++++k++aiv+t+vGq+qmwaaqfy++k+p++f++sg
  lcl|NCBI__GCF_900167125.1:WP_078716927.1 348 VDRVRSWAKEHPLTyAPSETGAIKPQFVVEKIYEITKGDAIVATEVGQNQMWAAQFYRFKSPNSFLSSG 416
                                               *************945566677*********************************************** PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG+G+PaalGa+ a p++ vv+++Gdgs+qm +qe++t+v  d+pvkivilnn +lGmv+qWqel
  lcl|NCBI__GCF_900167125.1:WP_078716927.1 417 GLGTMGYGFPAALGAQKAFPDKLVVNIAGDGSIQMCIQEMATAVCNDLPVKIVILNNGYLGMVRQWQEL 485
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmva 545
                                               fy++ y +t++ + +pdfvklaeayG++g r+++  ++e+ l++a++s++p+++dv+v+kee+v+Pmv+
  lcl|NCBI__GCF_900167125.1:WP_078716927.1 486 FYRKNYCQTCMDA-QPDFVKLAEAYGAEGYRVTESGDVESVLRQAFSSSKPAIVDVRVEKEENVYPMVP 553
                                               ************5.******************************************************* PP

                                 TIGR00118 546 pGagldelv 554
                                                Ga+++e++
  lcl|NCBI__GCF_900167125.1:WP_078716927.1 554 AGASITEML 562
                                               *******98 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.34
//
[ok]

This GapMind analysis is from Apr 10 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