Alignments for a candidate for ilvI in Thiohalospira halophila DSM 15071 HL 3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thiohalospira halophila DSM 15071 HL 3

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_093427731.1 BM272_RS05385 acetolactate synthase 3 large subunit

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



>NCBI__GCF_900112605.1:WP_093427731.1
          Length = 572

 Score =  796 bits (2056), Expect = 0.0
 Identities = 388/568 (68%), Positives = 459/568 (80%), Gaps = 3/568 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ G EI+V  L +EGVEY++GYPGGA L+IYD LH Q    HILVRHEQ A HAADGYA
Sbjct: 2   ELSGGEIIVQFLRDEGVEYIFGYPGGAALHIYDALHGQQDIRHILVRHEQGAGHAADGYA 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGK GV LVTSGPGVTNAVTGIATA++DSIPMVVI+G VPT  IG DAFQE D VGIT
Sbjct: 62  RATGKPGVMLVTSGPGVTNAVTGIATAHMDSIPMVVISGQVPTGVIGSDAFQEVDAVGIT 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACK--YEYPKSIDM 195
           RP VKHNFLVKDVRDLA+T+KKAF IA +GRPGPV+VD+PKDV+  + K  Y YP S+ +
Sbjct: 122 RPCVKHNFLVKDVRDLASTLKKAFHIATSGRPGPVLVDVPKDVTDPSVKIPYTYPSSVSL 181

Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLM 255
           RSYNPV +GH GQI++AV LL  A+RP IYTGGGVVL  AS  L ++    G+P+T TLM
Sbjct: 182 RSYNPVTRGHPGQIKRAVDLLLSAKRPMIYTGGGVVLGEASAALTEITRELGYPITQTLM 241

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLG++P +  QF+GMLGMHGTYEANMAM  CDVL A+GARFDDRV GN  HF+  AR II
Sbjct: 242 GLGSYPASDSQFLGMLGMHGTYEANMAMHECDVLFAVGARFDDRVTGNTEHFSPNAR-II 300

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           H+DIDPSSISK V+VD+PIVG+   VLQE++  +++ D  P   AL +WW QIEQWRS++
Sbjct: 301 HLDIDPSSISKNVRVDVPIVGDTDQVLQEMLRLMRSGDRHPDGAALKEWWGQIEQWRSLN 360

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
           CL YDRSSE+IKPQ V+EK+ E+T GDA++ SDVGQHQMWAAQFY F++PRRW+NSGGLG
Sbjct: 361 CLGYDRSSELIKPQMVIEKLAEVTGGDAYVSSDVGQHQMWAAQFYGFNKPRRWLNSGGLG 420

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG GLP A+G + A P+ +V  +TGE SIQMCIQELSTCLQY  P+KI +LNN Y+GMV
Sbjct: 421 TMGFGLPAAIGAQLADPQADVACVTGEASIQMCIQELSTCLQYMLPLKIINLNNRYMGMV 480

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE  Y++RYSHSYMDALPDFV+LAEAYGH G+RVE+  DVE ALREAF +KDR VFL
Sbjct: 481 RQWQEFFYESRYSHSYMDALPDFVRLAEAYGHTGLRVERPGDVEGALREAFAMKDRLVFL 540

Query: 556 DFQTDPTENVWPMVQAGKGISEMLLGAE 583
           DF TD TENV+PM++AGKG  EM L  +
Sbjct: 541 DFITDQTENVYPMIEAGKGHHEMHLSPD 568


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: 1048
Number of extensions: 37
Number of successful extensions: 3
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: 572
Length adjustment: 36
Effective length of query: 549
Effective length of database: 536
Effective search space:   294264
Effective search space used:   294264
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_093427731.1 BM272_RS05385 (acetolactate synthase 3 large subunit)
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.314077.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-263  858.9   0.0   8.6e-263  858.7   0.0    1.0  1  NCBI__GCF_900112605.1:WP_093427731.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093427731.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  858.7   0.0  8.6e-263  8.6e-263       1     554 [.       3     564 ..       3     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 858.7 bits;  conditional E-value: 8.6e-263
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           l+g+ei+v+ l++egve++fGyPGGa l+iydal+ +++++hilvrheq+a haadGyara+Gk+Gv+l+tsG
  NCBI__GCF_900112605.1:WP_093427731.1   3 LSGGEIIVQFLRDEGVEYIFGYPGGAALHIYDALHgQQDIRHILVRHEQGAGHAADGYARATGKPGVMLVTSG 75 
                                           689********************************************************************** PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PG tn+vtgiata++ds+P+vv++Gqv+t +iGsdafqe+d +Git+p++kh+flvk+++dl+++lk+af+ia
  NCBI__GCF_900112605.1:WP_093427731.1  76 PGVTNAVTGIATAHMDSIPMVVISGQVPTGVIGSDAFQEVDAVGITRPCVKHNFLVKDVRDLASTLKKAFHIA 148
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaea 216
                                           ++GrPGPvlvd+Pkdvt+++++++++  ++v+l++y+p ++gh+ qik+a++l+ +ak+P+++ GgGv+ +ea
  NCBI__GCF_900112605.1:WP_093427731.1 149 TSGRPGPVLVDVPKDVTDPSVKIPYTypSSVSLRSYNPVTRGHPGQIKRAVDLLLSAKRPMIYTGGGVVLGEA 221
                                           ********************999988779******************************************** PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           s+ l+e++ +l  p+t+tl+GlG++p+ + ++lgmlGmhGt+ean+a++e+d+l+avGarfddrvtgn ++f+
  NCBI__GCF_900112605.1:WP_093427731.1 222 SAALTEITRELGYPITQTLMGLGSYPASDSQFLGMLGMHGTYEANMAMHECDVLFAVGARFDDRVTGNTEHFS 294
                                           ************************************************************************* PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkekeWlekieewkkeyilkldee 357
                                           p+a+iih+didP++i+knv+vd+pivGd+ +vl+e+l+ +++          keW+ +ie+w++ ++l +d++
  NCBI__GCF_900112605.1:WP_093427731.1 295 PNARIIHLDIDPSSISKNVRVDVPIVGDTDQVLQEMLRLMRSGdrhpdGAALKEWWGQIEQWRSLNCLGYDRS 367
                                           **************************************9998755443223345******************* PP

                             TIGR00118 358 eesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeet 430
                                           +e ikPq vi++l +++ ++a+v++dvGqhqmwaaqfy ++kpr++++sgGlGtmGfGlPaa+Ga++a p+++
  NCBI__GCF_900112605.1:WP_093427731.1 368 SELIKPQMVIEKLAEVTGGDAYVSSDVGQHQMWAAQFYGFNKPRRWLNSGGLGTMGFGLPAAIGAQLADPQAD 440
                                           ************************************************************************* PP

                             TIGR00118 431 vvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGv 503
                                           v +vtG++s+qm +qelst+ +y +p+ki++lnn+++Gmv+qWqe+fye rys++++ + lpdfv+laeayG+
  NCBI__GCF_900112605.1:WP_093427731.1 441 VACVTGEASIQMCIQELSTCLQYMLPLKIINLNNRYMGMVRQWQEFFYESRYSHSYMDA-LPDFVRLAEAYGH 512
                                           **********************************************************5.************* PP

                             TIGR00118 504 kgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554
                                           +g+r+e+p ++e +l+ea+++k ++v+ld+  d++e+v+Pm+  G+g +e+ 
  NCBI__GCF_900112605.1:WP_093427731.1 513 TGLRVERPGDVEGALREAFAMKdRLVFLDFITDQTENVYPMIEAGKGHHEMH 564
                                           ******************9988799*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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: 00:00:00.01
# Mc/sec: 24.88
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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 original 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