Alignments for a candidate for ilvI in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thiohalomonas denitrificans HLD2

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_092997779.1 BLP65_RS11775 acetolactate synthase 3 large subunit

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



>NCBI__GCF_900102855.1:WP_092997779.1
          Length = 608

 Score =  791 bits (2043), Expect = 0.0
 Identities = 385/564 (68%), Positives = 462/564 (81%), Gaps = 2/564 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GAEILV  L +EGVE+V+GYPGGAVL+IYD + +Q   +H+LVRHEQAA HAADGYA
Sbjct: 45  ELTGAEILVRFLKDEGVEHVFGYPGGAVLHIYDAIFRQDDVKHVLVRHEQAATHAADGYA 104

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TNAVTGIATAY+DSIPMVV+TG V +  IG DAFQE D VGIT
Sbjct: 105 RSTGKPGVVLVTSGPGATNAVTGIATAYMDSIPMVVLTGQVNSALIGNDAFQEVDAVGIT 164

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP VKHNFLVKDV  LA+T+KKAF+IA TGRPGPVVVDIPKD++    KY +PK   +RS
Sbjct: 165 RPCVKHNFLVKDVAQLASTLKKAFYIATTGRPGPVVVDIPKDITALRTKYTHPKKAHLRS 224

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNPV KGH+GQI++AV L+  A+RP IY+GGGV+L NAS  L   A L G PVTNT MGL
Sbjct: 225 YNPVVKGHTGQIKRAVNLMLSAKRPLIYSGGGVILDNASKALTDFAKLLGFPVTNTSMGL 284

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G +P T KQF+GMLGMHGTYEAN+++ +CD+LIAIGARFDDRV GN A F   A KIIH+
Sbjct: 285 GGYPATDKQFLGMLGMHGTYEANLSVSHCDLLIAIGARFDDRVTGNIAKFAPHA-KIIHV 343

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+SISK VKVD+PIVG+V +VL+++   +K +   P   ALAKWWEQIE WR+ +CL
Sbjct: 344 DIDPASISKNVKVDVPIVGSVSNVLKDMNKLVKEAGKAPDGPALAKWWEQIEDWRAKECL 403

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           +YD+ S++IKPQYV++ ++E+TKGDAF+ SDVGQHQMWAAQFYKFD+PRRWINSGGLGTM
Sbjct: 404 RYDQKSDVIKPQYVIDTLYEVTKGDAFVTSDVGQHQMWAAQFYKFDKPRRWINSGGLGTM 463

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G+P AMG++ A P+ +V  ITGEGSIQM IQELSTCLQY  P+K+  LNN YLGMVRQ
Sbjct: 464 GFGMPAAMGVQFAHPKSKVACITGEGSIQMNIQELSTCLQYGLPIKVVCLNNRYLGMVRQ 523

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF-RLKDRTVFLD 556
           WQE  Y+ RYS+SYM++LPDFVKLAEAYGHVGM++EK  DV+PAL EAF + K+R VFL+
Sbjct: 524 WQEFFYEKRYSNSYMESLPDFVKLAEAYGHVGMQIEKPEDVKPALEEAFSKHKNRFVFLN 583

Query: 557 FQTDPTENVWPMVQAGKGISEMLL 580
           F TD TENV+PMV AG G+ EM+L
Sbjct: 584 FITDQTENVYPMVPAGAGLEEMIL 607


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: 1099
Number of extensions: 46
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: 608
Length adjustment: 37
Effective length of query: 548
Effective length of database: 571
Effective search space:   312908
Effective search space used:   312908
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_092997779.1 BLP65_RS11775 (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.22451.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-271  887.5   0.5   1.9e-271  887.3   0.5    1.0  1  lcl|NCBI__GCF_900102855.1:WP_092997779.1  BLP65_RS11775 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900102855.1:WP_092997779.1  BLP65_RS11775 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.3   0.5  1.9e-271  1.9e-271       1     555 [.      46     607 ..      46     608 .] 0.98

  Alignments for each domain:
  == domain 1  score: 887.3 bits;  conditional E-value: 1.9e-271
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaeilv+ lk+egve+vfGyPGGavl+iyda++ +++++h+lvrheqaa+haadGyar++Gk+Gvvl
  lcl|NCBI__GCF_900102855.1:WP_092997779.1  46 LTGAEILVRFLKDEGVEHVFGYPGGAVLHIYDAIFrQDDVKHVLVRHEQAATHAADGYARSTGKPGVVL 114
                                               68*********************************99******************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtgiatay+ds+P+vvltGqv+++liG+dafqe+d +Git+p++kh+flvk++++l+++
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 115 VTSGPGATNAVTGIATAYMDSIPMVVLTGQVNSALIGNDAFQEVDAVGITRPCVKHNFLVKDVAQLAST 183
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               lk+af+ia+tGrPGPv+vd+Pkd+t+  ++++ ++k +l++y+p vkgh+ qik+a++l+ +ak+P+++
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 184 LKKAFYIATTGRPGPVVVDIPKDITALRTKYTHPKKAHLRSYNPVVKGHTGQIKRAVNLMLSAKRPLIY 252
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGvi  +as+ l+++a+ l  pvt t +GlG++p++++++lgmlGmhGt+eanl+vs++dllia+Ga
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 253 SGGGVILDNASKALTDFAKLLGFPVTNTSMGLGGYPATDKQFLGMLGMHGTYEANLSVSHCDLLIAIGA 321
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkekeW 339
                                               rfddrvtgn+akfap+akiih+didPa+i+knvkvd+pivG + +vl+++ k +ke           +W
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 322 RFDDRVTGNIAKFAPHAKIIHVDIDPASISKNVKVDVPIVGSVSNVLKDMNKLVKEAgkapdGPALAKW 390
                                               **************************************************999999876654334456* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               +e+ie+w+++ +l++d++++ ikPq+vi++l++++k++a+vt+dvGqhqmwaaqfyk++kpr++i+sgG
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 391 WEQIEDWRAKECLRYDQKSDVIKPQYVIDTLYEVTKGDAFVTSDVGQHQMWAAQFYKFDKPRRWINSGG 459
                                               ********************************************************************* PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmGfG+Paa+G++ a+p+++v ++tG+gs+qmn+qelst+ +y++p+k+v+lnn++lGmv+qWqe+f
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 460 LGTMGFGMPAAMGVQFAHPKSKVACITGEGSIQMNIQELSTCLQYGLPIKVVCLNNRYLGMVRQWQEFF 528
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk..epvlldvevdkeeevlPmv 544
                                               ye+rys+++++s lpdfvklaeayG++g++iekpe+++ +l+ea++++  + v+l++  d++e+v+Pmv
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 529 YEKRYSNSYMES-LPDFVKLAEAYGHVGMQIEKPEDVKPALEEAFSKHknRFVFLNFITDQTENVYPMV 596
                                               ***********5.*******************************987645889**************** PP

                                 TIGR00118 545 apGagldelve 555
                                               + Gagl+e++ 
  lcl|NCBI__GCF_900102855.1:WP_092997779.1 597 PAGAGLEEMIL 607
                                               *********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (608 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: 13.41
//
[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