Alignments for a candidate for ilvI in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thiomicrospira cyclica ALM1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013834808.1 THICY_RS01270 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000214825.1:WP_013834808.1
          Length = 565

 Score =  768 bits (1983), Expect = 0.0
 Identities = 378/564 (67%), Positives = 442/564 (78%), Gaps = 2/564 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTK-FEHILVRHEQAAVHAADGY 76
           E+ GA+ILVH L +EGVE++WGYPGGA L IYD L    K  +HILVRHEQAAVHAADGY
Sbjct: 2   ELTGAQILVHFLEDEGVEHIWGYPGGAALPIYDALDTDAKELKHILVRHEQAAVHAADGY 61

Query: 77  ARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGI 136
           AR+TGK GV LVTSGPG TN VTGIATAY+DSIPM+V TG VPT  IG DAFQE DTVGI
Sbjct: 62  ARSTGKPGVVLVTSGPGATNTVTGIATAYMDSIPMIVFTGQVPTSLIGLDAFQEVDTVGI 121

Query: 137 TRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMR 196
           TRPIVKHNFLVKDV+DLA T+KKAF+IA TGRPGPVVVDIPKDV      Y Y + +++R
Sbjct: 122 TRPIVKHNFLVKDVKDLAITLKKAFYIATTGRPGPVVVDIPKDVQNATSTYVYTQEVELR 181

Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
           SY PV KGHSGQI+KAV L+  AERP  YTGGGVVL +AS+EL  L    G+P+T TLMG
Sbjct: 182 SYLPVTKGHSGQIKKAVELMLSAERPIFYTGGGVVLGDASEELVSLVKSLGYPITQTLMG 241

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
           LGA+P   +Q +GMLGMHGTYEAN+AM +CDVLIAIG+RFDDRV GN   F   A KIIH
Sbjct: 242 LGAYPAQDQQNLGMLGMHGTYEANLAMHHCDVLIAIGSRFDDRVTGNIEKFCPTA-KIIH 300

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           +DIDP+SISK V VD+PIVG VK V+ E+   +   +    +EAL  WW QI +WR ++C
Sbjct: 301 VDIDPASISKNVMVDVPIVGPVKQVVAEMNQHLAKLEKGRNKEALDAWWAQIAEWREMNC 360

Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436
           LK+D S   IKPQ  V+ +WE+TKGDA++ SDVGQHQM+AAQ+Y F++PRRWINSGGLGT
Sbjct: 361 LKFDESGTKIKPQAAVKAVWEVTKGDAYVTSDVGQHQMFAAQYYTFEKPRRWINSGGLGT 420

Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496
           MG GLP AMG++ A P+  VV ITGEGSIQM IQELSTCLQY  P+KI SLNNGYLGMVR
Sbjct: 421 MGFGLPAAMGVQMALPDATVVCITGEGSIQMNIQELSTCLQYGLPIKIVSLNNGYLGMVR 480

Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556
           QWQE  YD RYS SYMD+LPDFVKL E+YGHVG+R++    +   L EAF LKDR VF+D
Sbjct: 481 QWQEFFYDRRYSMSYMDSLPDFVKLTESYGHVGVRIDDPKTMRQQLEEAFALKDRLVFID 540

Query: 557 FQTDPTENVWPMVQAGKGISEMLL 580
             TDP ENV+PM+ AG G +EM+L
Sbjct: 541 ILTDPQENVYPMIPAGAGQNEMIL 564


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: 1007
Number of extensions: 32
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: 565
Length adjustment: 36
Effective length of query: 549
Effective length of database: 529
Effective search space:   290421
Effective search space used:   290421
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_013834808.1 THICY_RS01270 (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.4172780.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-267  872.5   2.3   6.5e-267  872.3   2.3    1.0  1  NCBI__GCF_000214825.1:WP_013834808.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214825.1:WP_013834808.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  872.3   2.3  6.5e-267  6.5e-267       1     555 [.       3     564 ..       3     565 .] 0.98

  Alignments for each domain:
  == domain 1  score: 872.3 bits;  conditional E-value: 6.5e-267
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                           l+ga+ilv+ l++egve+++GyPGGa lpiydal   ++el+hilvrheqaa+haadGyar++Gk+Gvvl+ts
  NCBI__GCF_000214825.1:WP_013834808.1   3 LTGAQILVHFLEDEGVEHIWGYPGGAALPIYDALDtdAKELKHILVRHEQAAVHAADGYARSTGKPGVVLVTS 75 
                                           68********************************988899********************************* PP

                             TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafei 144
                                           GPGatn+vtgiatay+ds+P++v+tGqv+tsliG dafqe+d +Git+p++kh+flvk+++dl+ +lk+af+i
  NCBI__GCF_000214825.1:WP_013834808.1  76 GPGATNTVTGIATAYMDSIPMIVFTGQVPTSLIGLDAFQEVDTVGITRPIVKHNFLVKDVKDLAITLKKAFYI 148
                                           ************************************************************************* PP

                             TIGR00118 145 astGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeas 217
                                           a+tGrPGPv+vd+Pkdv++a+ ++ ++++vel++y p +kgh  qikka+el+ +a++P+ + GgGv+ ++as
  NCBI__GCF_000214825.1:WP_013834808.1 149 ATTGRPGPVVVDIPKDVQNATSTYVYTQEVELRSYLPVTKGHSGQIKKAVELMLSAERPIFYTGGGVVLGDAS 221
                                           ************************************************************************* PP

                             TIGR00118 218 eelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap 290
                                           eel+ l++ l  p+t+tl+GlGa+p+++++ lgmlGmhGt+eanla++++d+lia+G rfddrvtgn++kf+p
  NCBI__GCF_000214825.1:WP_013834808.1 222 EELVSLVKSLGYPITQTLMGLGAYPAQDQQNLGMLGMHGTYEANLAMHHCDVLIAIGSRFDDRVTGNIEKFCP 294
                                           ************************************************************************* PP

                             TIGR00118 291 eakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldeee 358
                                            akiih+didPa+i+knv vd+pivG +k+v++e+ ++l +     +k+  + W+++i+ew++ ++lk+de+ 
  NCBI__GCF_000214825.1:WP_013834808.1 295 TAKIIHVDIDPASISKNVMVDVPIVGPVKQVVAEMNQHLAKLekgrNKEALDaWWAQIAEWREMNCLKFDESG 367
                                           ***********************************999988766643444457******************** PP

                             TIGR00118 359 esikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431
                                           ++ikPq+ +k++++++k++a+vt+dvGqhqm+aaq+y+++kpr++i+sgGlGtmGfGlPaa+G+++a p++tv
  NCBI__GCF_000214825.1:WP_013834808.1 368 TKIKPQAAVKAVWEVTKGDAYVTSDVGQHQMFAAQYYTFEKPRRWINSGGLGTMGFGLPAAMGVQMALPDATV 440
                                           ************************************************************************* PP

                             TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504
                                           v++tG+gs+qmn+qelst+ +y++p+kiv lnn +lGmv+qWqe+fy++rys +++ s lpdfvkl+e+yG++
  NCBI__GCF_000214825.1:WP_013834808.1 441 VCITGEGSIQMNIQELSTCLQYGLPIKIVSLNNGYLGMVRQWQEFFYDRRYSMSYMDS-LPDFVKLTESYGHV 512
                                           *********************************************************5.************** PP

                             TIGR00118 505 giriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelve 555
                                           g+ri +p+ + ++l+ea++ k ++v++d+  d +e+v+Pm++ Gag +e++ 
  NCBI__GCF_000214825.1:WP_013834808.1 513 GVRIDDPKTMRQQLEEAFALKdRLVFIDILTDPQENVYPMIPAGAGQNEMIL 564
                                           *****************9987699**************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (565 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: 14.03
//
[ok]

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

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