GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Desulforamulus ruminis DSM 2154

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013840432.1 DESRU_RS01875 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_000215085.1:WP_013840432.1
          Length = 553

 Score =  562 bits (1449), Expect = e-164
 Identities = 289/560 (51%), Positives = 368/560 (65%), Gaps = 10/560 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+  AE LV  L  EGVE V+GYPGGA+L +YD L+  +K +HIL RHEQ A HAA GYA
Sbjct: 2   EITCAEALVRCLELEGVELVFGYPGGAILPVYDALN-DSKIKHILTRHEQGAAHAASGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R TGKVGV + TSGPG TN VTG+A AY+DSIP+V ITG VPT  +G DAFQE D  GIT
Sbjct: 61  RTTGKVGVCMATSGPGATNLVTGLANAYMDSIPLVAITGQVPTSQVGTDAFQEVDITGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
            PI KHN+LVKD + L   +++AF IA TGRPGPV++D+PKDV+    K+ YP+ + ++ 
Sbjct: 121 IPITKHNYLVKDAKTLPLIVRRAFHIARTGRPGPVLIDLPKDVANTRIKFNYPEEVHLKG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  KGH  QI +A  L+  AERP IY GGGVV A AS+EL  LA     PV  TLMGL
Sbjct: 181 YKPTVKGHIAQINQAAKLMMQAERPVIYAGGGVVNAEASEELVWLAETLDAPVVTTLMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG  + F+GM G+HG   AN+A+ + D+LI +GARFDDRV G  A F   AR +IH+
Sbjct: 241 GAFPGDHRLFLGMPGLHGNLAANLAVTHSDLLITLGARFDDRVTGRIAGFAPGAR-VIHV 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+ ISK V   +PIVG+ K VL +L+ ++        ++    W EQ+  W+     
Sbjct: 300 DIDPAEISKNVISHLPIVGDTKKVLTDLLVRL-------DKKQNPGWIEQVSSWKEEHAH 352

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           +Y +  E++KPQYV+E+I+  +KGD  + +DVGQHQMW AQ + F EPR  + SGGLG M
Sbjct: 353 RYQQEGELLKPQYVIEEIYRHSKGDVIVSTDVGQHQMWVAQHFPFKEPRALVTSGGLGVM 412

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP A+G +   PEK VV +TG+GS QM + ELST  + + P+KI  LNN  LGMVRQ
Sbjct: 413 GFGLPGAIGAQIGRPEKTVVLVTGDGSFQMSLNELSTAAEQELPLKIVVLNNRCLGMVRQ 472

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
            QE   + RY+      +PDF  LA  YG  G  V    +++ AL EAF+     V +D 
Sbjct: 473 LQEFYCEKRYTAVDFGFVPDFAALARVYGFKGYTVNTAEELQSALTEAFQ-DPGPVLIDC 531

Query: 558 QTDPTENVWPMVQAGKGISE 577
             DP ENV PMV AGK I +
Sbjct: 532 SVDPNENVLPMVLAGKDICD 551


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: 909
Number of extensions: 35
Number of successful extensions: 6
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: 553
Length adjustment: 36
Effective length of query: 549
Effective length of database: 517
Effective search space:   283833
Effective search space used:   283833
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_013840432.1 DESRU_RS01875 (biosynthetic-type 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.3173901.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-251  820.1   0.0   5.2e-251  819.8   0.0    1.0  1  NCBI__GCF_000215085.1:WP_013840432.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013840432.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  819.8   0.0  5.2e-251  5.2e-251       2     549 ..       4     548 ..       3     552 .. 0.99

  Alignments for each domain:
  == domain 1  score: 819.8 bits;  conditional E-value: 5.2e-251
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                           + ae+lv+ l+ egve vfGyPGGa+lp+ydal ds+++hil+rheq+aahaa Gyar++GkvGv++atsGPG
  NCBI__GCF_000215085.1:WP_013840432.1   4 TCAEALVRCLELEGVELVFGYPGGAILPVYDALNDSKIKHILTRHEQGAAHAASGYARTTGKVGVCMATSGPG 76 
                                           679********************************************************************** PP

                             TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiast 147
                                           atnlvtg+a+ay+ds+Plv++tGqv+ts +G+dafqe+di+Git+p+tkh++lvk+a+ lp i+++af+ia t
  NCBI__GCF_000215085.1:WP_013840432.1  77 ATNLVTGLANAYMDSIPLVAITGQVPTSQVGTDAFQEVDITGITIPITKHNYLVKDAKTLPLIVRRAFHIART 149
                                           ************************************************************************* PP

                             TIGR00118 148 GrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseel 220
                                           GrPGPvl+dlPkdv+++ i+++++e+v+l+gykptvkgh +qi++a++l+++a++Pv+++GgGv+ aeaseel
  NCBI__GCF_000215085.1:WP_013840432.1 150 GRPGPVLIDLPKDVANTRIKFNYPEEVHLKGYKPTVKGHIAQINQAAKLMMQAERPVIYAGGGVVNAEASEEL 222
                                           ************************************************************************* PP

                             TIGR00118 221 kelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeak 293
                                           + lae+l++pv+ttl+GlGafp dh+l+lgm G+hG  +anlav+++dlli++Garfddrvtg +a fap a+
  NCBI__GCF_000215085.1:WP_013840432.1 223 VWLAETLDAPVVTTLMGLGAFPGDHRLFLGMPGLHGNLAANLAVTHSDLLITLGARFDDRVTGRIAGFAPGAR 295
                                           ************************************************************************* PP

                             TIGR00118 294 iihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkv 366
                                           +ih+didPaei+knv +++pivGd+kkvl++ll +l ++++    W+e++++wk+e+  ++++e e +kPq+v
  NCBI__GCF_000215085.1:WP_013840432.1 296 VIHVDIDPAEISKNVISHLPIVGDTKKVLTDLLVRLDKKQNPG--WIEQVSSWKEEHAHRYQQEGELLKPQYV 366
                                           ************************************9988877..**************************** PP

                             TIGR00118 367 ikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgs 439
                                           i+e+++  k+++iv+tdvGqhqmw+aq++++k+pr  +tsgGlG mGfGlP a+Ga+++ pe+tvv vtGdgs
  NCBI__GCF_000215085.1:WP_013840432.1 367 IEEIYRHSKGDVIVSTDVGQHQMWVAQHFPFKEPRALVTSGGLGVMGFGLPGAIGAQIGRPEKTVVLVTGDGS 439
                                           ************************************************************************* PP

                             TIGR00118 440 fqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpe 512
                                           fqm+l+elst++e ++p+kiv+lnn++lGmv+q qe++ e+ry+++ ++  +pdf++la+ yG kg ++++ e
  NCBI__GCF_000215085.1:WP_013840432.1 440 FQMSLNELSTAAEQELPLKIVVLNNRCLGMVRQLQEFYCEKRYTAVDFGF-VPDFAALARVYGFKGYTVNTAE 511
                                           *************************************************6.********************** PP

                             TIGR00118 513 eleeklkealeskepvlldvevdkeeevlPmvapGag 549
                                           el+++l+ea++  +pvl+d +vd +e+vlPmv  G+ 
  NCBI__GCF_000215085.1:WP_013840432.1 512 ELQSALTEAFQDPGPVLIDCSVDPNENVLPMVLAGKD 548
                                           *********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (553 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 21.81
//
[ok]

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

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:

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:

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:

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