Alignments for a candidate for ilvI in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Chlorobaculum tepidum TLS

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate NP_661518.1 CT0618 acetolactate synthase, large subunit

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



>NCBI__GCF_000006985.1:NP_661518.1
          Length = 573

 Score =  579 bits (1492), Expect = e-169
 Identities = 292/564 (51%), Positives = 380/564 (67%), Gaps = 7/564 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++IG+EI    L  E VEY++GYPGGA+L +Y+ LH     EHIL RHEQ A H A+GYA
Sbjct: 7   KLIGSEIFFECLRRENVEYIFGYPGGALLKVYETLHDVEDIEHILARHEQGATHMAEGYA 66

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATG+ GV LVTSGPG TN VTGI  AY+DS P+VV TG VP+  IG DAFQE D VGIT
Sbjct: 67  RATGRPGVVLVTSGPGATNTVTGITNAYMDSTPLVVFTGQVPSSLIGNDAFQEADIVGIT 126

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RPI KHNFLVKDVR+LA TI+KAF++A  GRPGPV+VD+PKDV    C +E+P+++D+R 
Sbjct: 127 RPITKHNFLVKDVRELATTIRKAFYLATNGRPGPVLVDMPKDVLNAECTFEWPENVDIRG 186

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           + P  K H+ Q+ KA  ++  A+RP  Y GGGV+ A AS ELR+LA     PVT TL GL
Sbjct: 187 FKPTIKCHANQVSKAAKMIAKAKRPLFYVGGGVISAEASAELRKLAIDQQIPVTMTLQGL 246

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG     +GMLGMHGTY AN A+ NCD+LIA+GARFDDRV G    F + A K IH 
Sbjct: 247 GAFPGDHPLSMGMLGMHGTYWANQAVSNCDLLIAVGARFDDRVTGKVDTFATHAYK-IHN 305

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+++ K +KVD+P+VG+ KD L  LI  +  S     RE  + W  +IE+WR    L
Sbjct: 306 DIDPTNVDKNIKVDLPVVGDSKDFLASLIEAMPKS-----REDRSAWLAEIEKWRKQCPL 360

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            Y+   + +K ++V++++   TKG A + +DVGQHQMW +Q+YKF EPR  I SGGLGTM
Sbjct: 361 DYEIEPDSLKTEFVIDEVSRQTKGHAVVVTDVGQHQMWTSQYYKFTEPRSIITSGGLGTM 420

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP A+G      ++ V+  +G+G + M IQE+ T +    P+KI  +NN YLGMVRQ
Sbjct: 421 GFGLPSAIGAAFGVTDRPVLLFSGDGGLMMNIQEMVTAVYNKLPIKIFLINNSYLGMVRQ 480

Query: 498 WQEIEYDNRYSHSYM-DALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556
           WQE+ +  +Y+ + +  + PDFVK+AEA+G   M          A+ EA    D  V +D
Sbjct: 481 WQELFHQEKYTFTDLASSNPDFVKVAEAFGCKAMSASNPEAARAAITEALAYNDGPVLVD 540

Query: 557 FQTDPTENVWPMVQAGKGISEMLL 580
           F+    + V+PMV AG  IS+MLL
Sbjct: 541 FRVIRKDMVFPMVPAGGSISDMLL 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: 949
Number of extensions: 38
Number of successful extensions: 4
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: 573
Length adjustment: 36
Effective length of query: 549
Effective length of database: 537
Effective search space:   294813
Effective search space used:   294813
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 NP_661518.1 CT0618 (acetolactate synthase, 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.10529.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.9e-243  794.9   0.0   2.2e-243  794.7   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_661518.1  CT0618 acetolactate synthase, la


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_661518.1  CT0618 acetolactate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  794.7   0.0  2.2e-243  2.2e-243       3     555 ..      10     564 ..       8     566 .. 0.99

  Alignments for each domain:
  == domain 1  score: 794.7 bits;  conditional E-value: 2.2e-243
                              TIGR00118   3 gaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                            g+ei+ e l++e+ve++fGyPGGa+l++y++l+  +++ehil+rheq+a+h+a+Gyara+G++Gvvl+tsGP
  lcl|NCBI__GCF_000006985.1:NP_661518.1  10 GSEIFFECLRRENVEYIFGYPGGALLKVYETLHdVEDIEHILARHEQGATHMAEGYARATGRPGVVLVTSGP 81 
                                            899******************************889************************************ PP

                              TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                            Gatn+vtgi++ay+ds+Plvv+tGqv++sliG+dafqe+di+Git+p+tkh+flvk++++l++++++af++a
  lcl|NCBI__GCF_000006985.1:NP_661518.1  82 GATNTVTGITNAYMDSTPLVVFTGQVPSSLIGNDAFQEADIVGITRPITKHNFLVKDVRELATTIRKAFYLA 153
                                            ************************************************************************ PP

                              TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeas 217
                                            + GrPGPvlvd+Pkdv +ae+++e +e+v+++g+kpt+k h +q+ ka+++i+kak+P+ +vGgGvi aeas
  lcl|NCBI__GCF_000006985.1:NP_661518.1 154 TNGRPGPVLVDMPKDVLNAECTFEWPENVDIRGFKPTIKCHANQVSKAAKMIAKAKRPLFYVGGGVISAEAS 225
                                            ************************************************************************ PP

                              TIGR00118 218 eelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                            +el++la  ++ipvt+tl+GlGafp dhpl++gmlGmhGt+ an avs++dlliavGarfddrvtg++++fa
  lcl|NCBI__GCF_000006985.1:NP_661518.1 226 AELRKLAIDQQIPVTMTLQGLGAFPGDHPLSMGMLGMHGTYWANQAVSNCDLLIAVGARFDDRVTGKVDTFA 297
                                            ************************************************************************ PP

                              TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesi 361
                                            ++a  ih didP++++kn+kvd+p+vGd+k  l+ l++++ + +++ + Wl++ie+w+k+++l ++ e +s+
  lcl|NCBI__GCF_000006985.1:NP_661518.1 298 THAYKIHNDIDPTNVDKNIKVDLPVVGDSKDFLASLIEAMPKSREDRSAWLAEIEKWRKQCPLDYEIEPDSL 369
                                            ****************************************999888888*********************** PP

                              TIGR00118 362 kPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvva 433
                                            k   vi+e+s+++k++a+v tdvGqhqmw++q+yk+++pr+ itsgGlGtmGfGlP+a+Ga  ++ +  v+ 
  lcl|NCBI__GCF_000006985.1:NP_661518.1 370 KTEFVIDEVSRQTKGHAVVVTDVGQHQMWTSQYYKFTEPRSIITSGGLGTMGFGLPSAIGAAFGVTDRPVLL 441
                                            ************************************************************************ PP

                              TIGR00118 434 vtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkg 505
                                             +Gdg+++mn+qe+ t+v  ++p+ki ++nn++lGmv+qWqelf++e+y+ t las++pdfvk+aea+G k+
  lcl|NCBI__GCF_000006985.1:NP_661518.1 442 FSGDGGLMMNIQEMVTAVYNKLPIKIFLINNSYLGMVRQWQELFHQEKYTFTDLASSNPDFVKVAEAFGCKA 513
                                            ************************************************************************ PP

                              TIGR00118 506 iriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelve 555
                                            +  ++pe + ++++eal+ + +pvl+d++v +++ v+Pmv+ G+++++++ 
  lcl|NCBI__GCF_000006985.1:NP_661518.1 514 MSASNPEAARAAITEALAYNdGPVLVDFRVIRKDMVFPMVPAGGSISDMLL 564
                                            *****************98879*************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (573 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.91
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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 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