Alignments for a candidate for ilvI in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfovibrio oxyclinae DSM 11498

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_018125421.1 B149_RS0112070 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000375485.1:WP_018125421.1
          Length = 563

 Score =  642 bits (1657), Expect = 0.0
 Identities = 324/567 (57%), Positives = 412/567 (72%), Gaps = 10/567 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           EM GA+IL+  L +EGV+ ++G+PGGAV+ IYDE+      EH+LVRHEQ A+HAADGYA
Sbjct: 2   EMTGAQILLKCLEKEGVDVMFGFPGGAVIDIYDEI-PNFSVEHVLVRHEQGAIHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGK GV LVTSGPG TN VTGIATAY+DSIP+VV TG VPT  IG DAFQE D VGIT
Sbjct: 61  RATGKAGVCLVTSGPGATNTVTGIATAYMDSIPVVVFTGQVPTPLIGNDAFQEVDIVGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KH++LV DV DLA T+++AFF+A +GRPGPV+VD+PKDV    CK+E+P+ + MRS
Sbjct: 121 RPCTKHSYLVTDVNDLARTVRQAFFLARSGRPGPVLVDLPKDVMNRKCKFEWPEDVSMRS 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  K H GQ+RK   L++ AERP IY+GGGVVL+ + +ELR L+   G PVT+TLMGL
Sbjct: 181 YNPNVKPHVGQVRKVAKLIRNAERPLIYSGGGVVLSKSHEELRWLSDKLGIPVTSTLMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GA+PG    ++GMLGMHGTY ANMA+ +CD+L+A+GARFDDRV G  + F   A  I+HI
Sbjct: 241 GAYPGDGDNWLGMLGMHGTYAANMAVNHCDLLLAVGARFDDRVTGKVSTFAPHA-TIVHI 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKA----SDIKPKREALAKWWEQIEQWRS 373
           D+DP+SI K V V +P+V + K  L  L  +++A     D   K +   +WW Q+++W  
Sbjct: 300 DVDPTSIQKNVSVHVPLVADCKSALASLKKEMQALHDQEDWSLKHD---EWWCQLKEWDR 356

Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433
           +  L Y+   + IKPQYVVE I ++T+G+A I ++VGQ+QMWAAQF K  EP R++ SGG
Sbjct: 357 MHPLTYNDVEDGIKPQYVVEMIQDITEGEAIIATEVGQNQMWAAQFLKVKEPNRFLTSGG 416

Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493
           LGTMG G P AMG +KAFP+K VV I G+GSIQM IQE+ T +    PVKI  LNNG+LG
Sbjct: 417 LGTMGYGFPAAMGAQKAFPDKLVVDIAGDGSIQMNIQEMMTVVCNKLPVKIVILNNGFLG 476

Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553
           MVRQWQE+ YD  Y  + MDA PDFVKLAEAYG  G R+ +  DV P L++AF   D+  
Sbjct: 477 MVRQWQELFYDRNYCETCMDAQPDFVKLAEAYGAEGYRITQKKDVGPVLKKAFS-TDKPA 535

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLL 580
            +D +    ENV+PMV AG  ++EMLL
Sbjct: 536 IIDVRVTNEENVYPMVPAGASLTEMLL 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: 945
Number of extensions: 35
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: 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 WP_018125421.1 B149_RS0112070 (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.8068.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-257  838.8   0.3   1.1e-256  838.6   0.3    1.0  1  lcl|NCBI__GCF_000375485.1:WP_018125421.1  B149_RS0112070 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018125421.1  B149_RS0112070 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  838.6   0.3  1.1e-256  1.1e-256       1     554 [.       3     561 ..       3     563 .] 0.98

  Alignments for each domain:
  == domain 1  score: 838.6 bits;  conditional E-value: 1.1e-256
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++ga+il++ l+kegv+++fG+PGGav++iyd++ +  +eh+lvrheq+a+haadGyara+Gk+Gv+l+
  lcl|NCBI__GCF_000375485.1:WP_018125421.1   3 MTGAQILLKCLEKEGVDVMFGFPGGAVIDIYDEIPNFSVEHVLVRHEQGAIHAADGYARATGKAGVCLV 71 
                                               79******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgiatay+ds+P+vv+tGqv+t liG+dafqe+di+Git+p+tkhs+lv++++dl++++
  lcl|NCBI__GCF_000375485.1:WP_018125421.1  72 TSGPGATNTVTGIATAYMDSIPVVVFTGQVPTPLIGNDAFQEVDIVGITRPCTKHSYLVTDVNDLARTV 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               ++af +a +GrPGPvlvdlPkdv+++++++e +e+v++++y+p+vk+h  q++k+++li++a++P+++ 
  lcl|NCBI__GCF_000375485.1:WP_018125421.1 141 RQAFFLARSGRPGPVLVDLPKDVMNRKCKFEWPEDVSMRSYNPNVKPHVGQVRKVAKLIRNAERPLIYS 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv+ ++++eel+ l+++l ipvt+tl+GlGa+p d  + lgmlGmhGt++an+av+++dll+avGar
  lcl|NCBI__GCF_000375485.1:WP_018125421.1 210 GGGVVLSKSHEELRWLSDKLGIPVTSTLMGLGAYPGDGDNWLGMLGMHGTYAANMAVNHCDLLLAVGAR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee......ekkekeW 339
                                               fddrvtg++++fap+a+i+hid+dP++i+knv+v++p+v d+k+ l+ l k++++       + k+ eW
  lcl|NCBI__GCF_000375485.1:WP_018125421.1 279 FDDRVTGKVSTFAPHATIVHIDVDPTSIQKNVSVHVPLVADCKSALASLKKEMQALhdqedwSLKHDEW 347
                                               ***********************************************999998887555555455567* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               + +++ew + ++l+++  e+ ikPq+v++ ++ ++++eai++t+vGq+qmwaaqf+k+k+p++f+tsgG
  lcl|NCBI__GCF_000375485.1:WP_018125421.1 348 WCQLKEWDRMHPLTYNDVEDGIKPQYVVEMIQDITEGEAIIATEVGQNQMWAAQFLKVKEPNRFLTSGG 416
                                               ********************************************************************* PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmG+G+Paa+Ga+ a p++ vv+++Gdgs+qmn+qe+ t+v  ++pvkivilnn +lGmv+qWqelf
  lcl|NCBI__GCF_000375485.1:WP_018125421.1 417 LGTMGYGFPAAMGAQKAFPDKLVVDIAGDGSIQMNIQEMMTVVCNKLPVKIVILNNGFLGMVRQWQELF 485
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546
                                               y++ y et++ + +pdfvklaeayG++g ri++++++   lk+a+++++p+++dv+v +ee+v+Pmv+ 
  lcl|NCBI__GCF_000375485.1:WP_018125421.1 486 YDRNYCETCMDA-QPDFVKLAEAYGAEGYRITQKKDVGPVLKKAFSTDKPAIIDVRVTNEENVYPMVPA 553
                                               ***********5.******************************************************** PP

                                 TIGR00118 547 Gagldelv 554
                                               Ga+l+e++
  lcl|NCBI__GCF_000375485.1:WP_018125421.1 554 GASLTEML 561
                                               ******98 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.68
//
[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