Alignments for a candidate for ilvI in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfitobacterium hafniense DCB-2

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_005816732.1 DHAF_RS12310 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000021925.1:WP_005816732.1
          Length = 561

 Score =  548 bits (1412), Expect = e-160
 Identities = 283/559 (50%), Positives = 373/559 (66%), Gaps = 12/559 (2%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GA +L+ +L +EGVE ++GYPGGAVL IYD L   +   H+L RHEQ A+HAAD +AR +
Sbjct: 13  GAALLLDSLVQEGVEVMFGYPGGAVLPIYDALIN-SPIRHLLPRHEQTAIHAADAFARVS 71

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGV L TSGPG TN VTGIA AY+DSIP+V++TG VPT  +G D+FQE D  GIT PI
Sbjct: 72  GKVGVCLATSGPGATNLVTGIANAYMDSIPVVILTGQVPTSLLGTDSFQEVDITGITLPI 131

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            KH++LVKD R +   +K+AF+IA+TGRPGPV++D+PK+V         P  ++++SY  
Sbjct: 132 TKHSYLVKDPRQIPRIVKEAFYIASTGRPGPVLIDLPKNVLAATDVRPAPAELNLKSYKY 191

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
             KG++GQI +A  ++  ++RP +Y GGGV+ A AS+ L+Q+      PV  TLMG+G+ 
Sbjct: 192 FTKGNAGQIEEAARVIAQSQRPVLYAGGGVITAGASEILQQVVERANLPVVTTLMGIGSL 251

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
           P      +GM+GMHGT  AN A+ +CD+LIAIG RFDDRV     H  +   KIIHIDID
Sbjct: 252 PTNHPNVLGMVGMHGTVTANYAVDDCDLLIAIGVRFDDRVTSGLGHRFATKAKIIHIDID 311

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLKYD 380
           P+ I K  +  +PIVGN K VL+EL++++   +I P       WWEQI  W+  + LK D
Sbjct: 312 PAEIGKVARTKVPIVGNAKLVLEELLSKVSKPEISP-------WWEQIRLWQE-EKLKTD 363

Query: 381 RSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMGVG 440
             +  + PQ ++E + E+   +  + +DVGQHQMWAAQ Y    PR +I SGGLGTMG G
Sbjct: 364 NPN--LNPQVIIETLGEIAGEETIVTTDVGQHQMWAAQGYPVPAPRHFITSGGLGTMGFG 421

Query: 441 LPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQWQE 500
           LP A+G + A PE  V  +TG+GS QM IQEL+T +QY  PVKI  +NNG LGMVRQ Q 
Sbjct: 422 LPAALGAQVAAPESTVFLVTGDGSFQMSIQELATAVQYQLPVKIILMNNGVLGMVRQLQM 481

Query: 501 IEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQTD 560
           +  D RYS   + A PDF+K+AEAYG  G+RV +TS+V  AL EA       V +DF   
Sbjct: 482 VFCDERYSQIQLTANPDFIKIAEAYGIRGIRVTETSEVRNALLEAIN-HPGPVLMDFIIS 540

Query: 561 PTENVWPMVQAGKGISEML 579
             E V PMV  GKG++EML
Sbjct: 541 EDEVVSPMVPPGKGLTEML 559


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: 887
Number of extensions: 38
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: 561
Length adjustment: 36
Effective length of query: 549
Effective length of database: 525
Effective search space:   288225
Effective search space used:   288225
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_005816732.1 DHAF_RS12310 (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.4877.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-251  819.6   0.6   6.8e-251  819.5   0.6    1.0  1  lcl|NCBI__GCF_000021925.1:WP_005816732.1  DHAF_RS12310 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_005816732.1  DHAF_RS12310 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  819.5   0.6  6.8e-251  6.8e-251       2     555 ..      12     560 ..      11     561 .] 0.99

  Alignments for each domain:
  == domain 1  score: 819.5 bits;  conditional E-value: 6.8e-251
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +ga +l++sl +egve++fGyPGGavlpiydal +s ++h+l+rheq+a+haad +ar+sGkvGv+lat
  lcl|NCBI__GCF_000021925.1:WP_005816732.1  12 TGAALLLDSLVQEGVEVMFGYPGGAVLPIYDALINSPIRHLLPRHEQTAIHAADAFARVSGKVGVCLAT 80 
                                               799****************************************************************** PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatnlvtgia+ay+ds+P+v+ltGqv+tsl+G+d+fqe+di+Gitlp+tkhs+lvk+++++p+i+k
  lcl|NCBI__GCF_000021925.1:WP_005816732.1  81 SGPGATNLVTGIANAYMDSIPVVILTGQVPTSLLGTDSFQEVDITGITLPITKHSYLVKDPRQIPRIVK 149
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               eaf+iastGrPGPvl+dlPk+v +a+   + +++++l++yk  +kg+  qi++a+ +i+++++Pvl++G
  lcl|NCBI__GCF_000021925.1:WP_005816732.1 150 EAFYIASTGRPGPVLIDLPKNVLAATDVRPAPAELNLKSYKYFTKGNAGQIEEAARVIAQSQRPVLYAG 218
                                               *************************999999************************************** PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gGvi+a+ase l++++er+++pv+ttl+G+G++p +hp+ lgm+GmhGt +an+av+++dllia+G+rf
  lcl|NCBI__GCF_000021925.1:WP_005816732.1 219 GGVITAGASEILQQVVERANLPVVTTLMGIGSLPTNHPNVLGMVGMHGTVTANYAVDDCDLLIAIGVRF 287
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnl.akfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               ddrvt+ l ++fa++akiihididPaeigk+ ++++pivG+ak vleell+k+++ e +   W+e+i+ 
  lcl|NCBI__GCF_000021925.1:WP_005816732.1 288 DDRVTSGLgHRFATKAKIIHIDIDPAEIGKVARTKVPIVGNAKLVLEELLSKVSKPEISP--WWEQIRL 354
                                               *****999457*******************************************999988..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               w++e++   ++++ +++Pq +i++l +++ +e+ivttdvGqhqmwaaq y++ +pr+fitsgGlGtmGf
  lcl|NCBI__GCF_000021925.1:WP_005816732.1 355 WQEEKL---KTDNPNLNPQVIIETLGEIAGEETIVTTDVGQHQMWAAQGYPVPAPRHFITSGGLGTMGF 420
                                               **9986...889999****************************************************** PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               GlPaalGa+va pe+tv  vtGdgsfqm++qel+t+v+y++pvki+++nn +lGmv+q q +f +erys
  lcl|NCBI__GCF_000021925.1:WP_005816732.1 421 GLPAALGAQVAAPESTVFLVTGDGSFQMSIQELATAVQYQLPVKIILMNNGVLGMVRQLQMVFCDERYS 489
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               + +l++ +pdf+k+aeayG++gir+++ +e+ ++l ea+++ +pvl+d+ + ++e v Pmv+pG+gl+e
  lcl|NCBI__GCF_000021925.1:WP_005816732.1 490 QIQLTA-NPDFIKIAEAYGIRGIRVTETSEVRNALLEAINHPGPVLMDFIISEDEVVSPMVPPGKGLTE 557
                                               *****5.************************************************************** PP

                                 TIGR00118 553 lve 555
                                               +++
  lcl|NCBI__GCF_000021925.1:WP_005816732.1 558 MLG 560
                                               *85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (561 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: 9.19
//
[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