Alignments for a candidate for ilvI in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Heliobacterium modesticaldum Ice1; ATCC 51547

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_083765181.1 HM1_RS06885 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000019165.1:WP_083765181.1
          Length = 576

 Score =  528 bits (1360), Expect = e-154
 Identities = 291/574 (50%), Positives = 371/574 (64%), Gaps = 15/574 (2%)

Query: 9   ADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQA 68
           AD+       + GA+ L+  L E GVE ++GYPGG+VL IYD L  ++   HILVR EQ 
Sbjct: 14  ADTGRGEWNALNGAQALLKCLEENGVEVIFGYPGGSVLPIYDAL-LESPIRHILVRCEQG 72

Query: 69  AVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAF 128
           A HAA+G+ARA GK GV L TSGPG TN VTGIA AY+DSIPMV+ITG VPT  +G DAF
Sbjct: 73  AAHAANGFARAAGKPGVCLATSGPGATNLVTGIANAYMDSIPMVIITGQVPTSMVGTDAF 132

Query: 129 QECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKY- 187
           QE D  GIT PI KHN+LVKDV D+   + +AF IA+TGRPGPV++DIPKDV    C   
Sbjct: 133 QEVDITGITMPITKHNYLVKDVGDIPRVVYEAFHIASTGRPGPVLIDIPKDVLSAECSRC 192

Query: 188 -EYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALT 246
            E P +ID+R Y P  KGH  QI+ A  L+Q A+RP I  GGG++LANA+ EL +LA   
Sbjct: 193 GEKP-AIDIRGYRPNVKGHPSQIKNAAKLIQEAKRPVIMVGGGIILANAAQELTELALSA 251

Query: 247 GHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAH 306
             PVT TLMG+GAFP T    +GM+GMHGT  AN A+   D+LI IG RF DR  GN A 
Sbjct: 252 QIPVTTTLMGIGAFPETHPLSLGMVGMHGTPYANRAVSQADLLIGIGVRFGDRATGNVAK 311

Query: 307 FTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWE 366
           F   A KIIHIDIDP+ I K   +D+PIVG+ + VLQ+L      + +KP     A+W E
Sbjct: 312 FARDA-KIIHIDIDPAEIGKNADIDVPIVGDARLVLQQL------NQLKPAPNH-AEWLE 363

Query: 367 QIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPR 426
           Q+ Q ++ + LKY + S  +  QYV+EK  ++T+  A++ +DVGQHQ+WAA  YKF +P 
Sbjct: 364 QVAQLKAQNPLKYPKQS--LTAQYVIEKAGDMTRDQAWVATDVGQHQIWAALHYKFIKPG 421

Query: 427 RWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICS 486
           R++ S GLGTMG GLP A G++ A P+  V+  TG+GSIQM +QEL T  Q + P+KI  
Sbjct: 422 RFVTSAGLGTMGYGLPAANGLQTARPDDMVILFTGDGSIQMQMQELGTARQENLPLKIIL 481

Query: 487 LNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF 546
            NN  LGMVRQ Q      RYS   +   P F  +A AYG     V +  +VE  LREAF
Sbjct: 482 FNNNALGMVRQLQHFYCGKRYSGVKLTFNPSFESIAAAYGIRYFAVTRLEEVEATLREAF 541

Query: 547 RLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLL 580
                 V ++  TD  + V+P V  GKG+ E++L
Sbjct: 542 -AHPGIVLVEVMTDENDMVYPTVLGGKGLDEIIL 574


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: 894
Number of extensions: 41
Number of successful extensions: 7
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: 576
Length adjustment: 36
Effective length of query: 549
Effective length of database: 540
Effective search space:   296460
Effective search space used:   296460
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_083765181.1 HM1_RS06885 (acetolactate synthase, large subunit, biosynthetic type)
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.2529.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-242  790.5   0.5   4.5e-242  790.4   0.5    1.0  1  lcl|NCBI__GCF_000019165.1:WP_083765181.1  HM1_RS06885 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_083765181.1  HM1_RS06885 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  790.4   0.5  4.5e-242  4.5e-242       1     555 [.      24     574 ..      24     576 .] 0.97

  Alignments for each domain:
  == domain 1  score: 790.4 bits;  conditional E-value: 4.5e-242
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+ga++l++ l+++gve++fGyPGG+vlpiydal +s ++hilvr eq+aahaa+G+ara+Gk+Gv+la
  lcl|NCBI__GCF_000019165.1:WP_083765181.1  24 LNGAQALLKCLEENGVEVIFGYPGGSVLPIYDALLESPIRHILVRCEQGAAHAANGFARAAGKPGVCLA 92 
                                               579****************************************************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtgia+ay+ds+P+v++tGqv+ts++G+dafqe+di+Git+p+tkh++lvk++ d+p+++
  lcl|NCBI__GCF_000019165.1:WP_083765181.1  93 TSGPGATNLVTGIANAYMDSIPMVIITGQVPTSMVGTDAFQEVDITGITMPITKHNYLVKDVGDIPRVV 161
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakkPvll 206
                                                eaf+iastGrPGPvl+d+Pkdv +ae++   e   ++++gy+p+vkgh+ qik+a++li++ak+Pv++
  lcl|NCBI__GCF_000019165.1:WP_083765181.1 162 YEAFHIASTGRPGPVLIDIPKDVLSAECSRCGEkPAIDIRGYRPNVKGHPSQIKNAAKLIQEAKRPVIM 230
                                               ***************************988766489********************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               vGgG+i a+a +el+ela  ++ipvtttl+G+Gafpe+hpl+lgm+GmhGt +an avs+adlli++G+
  lcl|NCBI__GCF_000019165.1:WP_083765181.1 231 VGGGIILANAAQELTELALSAQIPVTTTLMGIGAFPETHPLSLGMVGMHGTPYANRAVSQADLLIGIGV 299
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekie 344
                                               rf dr tgn+akfa++akiihididPaeigkn   d+pivGda+ vl++l +   + ++   eWle+++
  lcl|NCBI__GCF_000019165.1:WP_083765181.1 300 RFGDRATGNVAKFARDAKIIHIDIDPAEIGKNADIDVPIVGDARLVLQQLNQLKPAPNHA--EWLEQVA 366
                                               *************************************************97665544444..4****** PP

                                 TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413
                                               ++k++++lk  + ++s+  q+vi++   +++d+a v+tdvGqhq+waa +yk+ kp +f+ts+GlGtmG
  lcl|NCBI__GCF_000019165.1:WP_083765181.1 367 QLKAQNPLK--YPKQSLTAQYVIEKAGDMTRDQAWVATDVGQHQIWAALHYKFIKPGRFVTSAGLGTMG 433
                                               *******65..5678899*************************************************** PP

                                 TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482
                                               +GlPaa G + a p++ v+  tGdgs+qm++qel t+++ ++p+ki+++nn+ lGmv+q q+++  +ry
  lcl|NCBI__GCF_000019165.1:WP_083765181.1 434 YGLPAANGLQTARPDDMVILFTGDGSIQMQMQELGTARQENLPLKIILFNNNALGMVRQLQHFYCGKRY 502
                                               ********************************************************************* PP

                                 TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagld 551
                                               s +kl+  +p f+ +a ayG++   +++ ee+e+ l+ea+++ + vl++v  d+++ v+P v  G+gld
  lcl|NCBI__GCF_000019165.1:WP_083765181.1 503 SGVKLTF-NPSFESIAAAYGIRYFAVTRLEEVEATLREAFAHPGIVLVEVMTDENDMVYPTVLGGKGLD 570
                                               ******6.9************************************************************ PP

                                 TIGR00118 552 elve 555
                                               e++ 
  lcl|NCBI__GCF_000019165.1:WP_083765181.1 571 EIIL 574
                                               *996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (576 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.75
//
[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