Alignments for a candidate for ilvI in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thermithiobacillus tepidarius DSM 3134

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_081662815.1 G579_RS0113910 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000423825.1:WP_081662815.1
          Length = 588

 Score =  803 bits (2073), Expect = 0.0
 Identities = 389/563 (69%), Positives = 458/563 (81%), Gaps = 1/563 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GAEI+V  LAEEGVE+V+GYPGGAVL IYD   +Q + +H+LVRHEQA VHAADGYA
Sbjct: 26  ELTGAEIVVRCLAEEGVEFVFGYPGGAVLNIYDAFFQQDRVKHVLVRHEQAGVHAADGYA 85

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGKVGVALVTSGPG TNAVTGIATAY+DSIP+VVITG VP   IG DAFQE DTVGIT
Sbjct: 86  RATGKVGVALVTSGPGATNAVTGIATAYMDSIPLVVITGQVPVPLIGNDAFQEVDTVGIT 145

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHNFLVKDVRDLA TIK AF+IA++GRPGPVVVDIPKD++ +   + YP+++++RS
Sbjct: 146 RPCTKHNFLVKDVRDLAETIKAAFYIASSGRPGPVVVDIPKDITIHKAPFHYPEAVNLRS 205

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  KGH GQIRKAV L+  A+RP IYTGGGVVL   S EL QL    G+P TNTLMGL
Sbjct: 206 YKPTVKGHPGQIRKAVQLMLSAKRPMIYTGGGVVLGEGSAELTQLVRRLGYPCTNTLMGL 265

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GA+P T   FVGMLGMHGTYEANM M +CDVLIAIGARFDDRV GN   F  +A KIIHI
Sbjct: 266 GAYPATDPLFVGMLGMHGTYEANMGMHHCDVLIAIGARFDDRVTGNLEKFCPEA-KIIHI 324

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           D+DP+SISK VKVDIPIVG VK VL E+   +   D +P  EALA WWEQI +WR+ +CL
Sbjct: 325 DVDPASISKNVKVDIPIVGEVKQVLAEMNQVLDQMDARPDAEALAAWWEQINEWRARECL 384

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           +Y+ S EIIKPQ+V++K++EL++G A++ SDVGQHQMWAAQ+Y+FD PRRWINSGGLGTM
Sbjct: 385 RYEWSDEIIKPQFVIQKLYELSQGGAYVTSDVGQHQMWAAQYYQFDRPRRWINSGGLGTM 444

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP AMG + A P++ V+ +TGE SIQM IQELSTCLQY  P+K+  LNN Y+GMVRQ
Sbjct: 445 GFGLPAAMGAQLAHPDETVICVTGEASIQMNIQELSTCLQYHLPIKVALLNNRYMGMVRQ 504

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE  Y +RY+ SYMDALPDFVKLAE+YGH+G+R EK SDVEP +REA +LKDR VF+DF
Sbjct: 505 WQEFFYGSRYAMSYMDALPDFVKLAESYGHIGLRAEKPSDVEPVIREALKLKDRLVFMDF 564

Query: 558 QTDPTENVWPMVQAGKGISEMLL 580
           + DP ENV+PMV AG G+SEM+L
Sbjct: 565 RVDPAENVYPMVPAGAGLSEMIL 587


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: 1046
Number of extensions: 34
Number of successful extensions: 2
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: 588
Length adjustment: 37
Effective length of query: 548
Effective length of database: 551
Effective search space:   301948
Effective search space used:   301948
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_081662815.1 G579_RS0113910 (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.2787.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-268  878.0   0.1   1.4e-268  877.8   0.1    1.0  1  lcl|NCBI__GCF_000423825.1:WP_081662815.1  G579_RS0113910 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000423825.1:WP_081662815.1  G579_RS0113910 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  877.8   0.1  1.4e-268  1.4e-268       1     555 [.      27     587 ..      27     588 .] 0.98

  Alignments for each domain:
  == domain 1  score: 877.8 bits;  conditional E-value: 1.4e-268
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaei+v+ l +egve vfGyPGGavl+iyda++ ++ ++h+lvrheqa +haadGyara+GkvGv+l
  lcl|NCBI__GCF_000423825.1:WP_081662815.1  27 LTGAEIVVRCLAEEGVEFVFGYPGGAVLNIYDAFFqQDRVKHVLVRHEQAGVHAADGYARATGKVGVAL 95 
                                               68*********************************8999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtgiatay+ds+Plvv+tGqv+  liG+dafqe+d +Git+p+tkh+flvk+++dl+e+
  lcl|NCBI__GCF_000423825.1:WP_081662815.1  96 VTSGPGATNAVTGIATAYMDSIPLVVITGQVPVPLIGNDAFQEVDTVGITRPCTKHNFLVKDVRDLAET 164
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               +k+af+ias+GrPGPv+vd+Pkd+t ++  ++++e v+l++ykptvkgh+ qi+ka++l+ +ak+P+++
  lcl|NCBI__GCF_000423825.1:WP_081662815.1 165 IKAAFYIASSGRPGPVVVDIPKDITIHKAPFHYPEAVNLRSYKPTVKGHPGQIRKAVQLMLSAKRPMIY 233
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGv+ +e+s+el++l+ rl  p t tl+GlGa+p+++pl++gmlGmhGt+ean+ ++++d+lia+Ga
  lcl|NCBI__GCF_000423825.1:WP_081662815.1 234 TGGGVVLGEGSAELTQLVRRLGYPCTNTLMGLGAYPATDPLFVGMLGMHGTYEANMGMHHCDVLIAIGA 302
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.W 339
                                               rfddrvtgnl+kf+peakiihid+dPa+i+knvkvdipivG++k+vl+e+ + l ++    + +    W
  lcl|NCBI__GCF_000423825.1:WP_081662815.1 303 RFDDRVTGNLEKFCPEAKIIHIDVDPASISKNVKVDIPIVGEVKQVLAEMNQVLDQMdarpDAEALAaW 371
                                               **************************************************999988876653333347* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               +e+i+ew+++ +l+++ ++e ikPq vi++l++l ++ a+vt+dvGqhqmwaaq+y++++pr++i+sgG
  lcl|NCBI__GCF_000423825.1:WP_081662815.1 372 WEQINEWRARECLRYEWSDEIIKPQFVIQKLYELSQGGAYVTSDVGQHQMWAAQYYQFDRPRRWINSGG 440
                                               ********************************************************************* PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmGfGlPaa+Ga++a+p+etv++vtG++s+qmn+qelst+ +y++p+k+ +lnn+++Gmv+qWqe+f
  lcl|NCBI__GCF_000423825.1:WP_081662815.1 441 LGTMGFGLPAAMGAQLAHPDETVICVTGEASIQMNIQELSTCLQYHLPIKVALLNNRYMGMVRQWQEFF 509
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmva 545
                                               y  ry+ +++ + lpdfvklae+yG+ g+r ekp+++e  ++eal+ k ++v++d++vd  e+v+Pmv+
  lcl|NCBI__GCF_000423825.1:WP_081662815.1 510 YGSRYAMSYMDA-LPDFVKLAESYGHIGLRAEKPSDVEPVIREALKLKdRLVFMDFRVDPAENVYPMVP 577
                                               ***********5.********************************988699****************** PP

                                 TIGR00118 546 pGagldelve 555
                                                Gagl+e++ 
  lcl|NCBI__GCF_000423825.1:WP_081662815.1 578 AGAGLSEMIL 587
                                               ********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (588 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: 00:00:00.02
# Mc/sec: 11.79
//
[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