GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Trichormus variabilis ATCC 29413

Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_011317028.1 AVA_RS00670 ketol-acid reductoisomerase

Query= BRENDA::C8WR67
         (344 letters)



>NCBI__GCF_000204075.1:WP_011317028.1
          Length = 331

 Score =  448 bits (1152), Expect = e-130
 Identities = 221/329 (67%), Positives = 266/329 (80%), Gaps = 1/329 (0%)

Query: 1   MEKIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSSWA-KAEAD 59
           M ++YYD D ++  LA K IA+IGYGSQGHAHA NL+DSG +V++GL PGS  A KA+A 
Sbjct: 1   MARMYYDEDANLDLLAGKTIAIIGYGSQGHAHALNLKDSGLNVIVGLYPGSKSAEKAQAA 60

Query: 60  GFRVMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPP 119
           G  V  V +A   +D IMILLPDE Q  VY+ EI P L  G  LAFAHGFNIHF Q+ PP
Sbjct: 61  GLTVKNVADAANVADFIMILLPDEVQKTVYKNEIEPNLQEGNTLAFAHGFNIHFGQVVPP 120

Query: 120 KDVDVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGIL 179
            +VDV MVAPKGPGHLVRR YE G GVPAL AV+QDASG+A+D AL+YA+GIG  R G+L
Sbjct: 121 ANVDVVMVAPKGPGHLVRRTYEQGQGVPALFAVYQDASGKARDRALSYAKGIGGTRGGVL 180

Query: 180 TTTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIY 239
            TTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPE+AYFECLHE+KLIVDL+ 
Sbjct: 181 ETTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPELAYFECLHEVKLIVDLVV 240

Query: 240 EGGLEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRP 299
           EGGL  MR SIS+TA++GD+T GPRI+NE+TK EMR++L++IQSG FA+ ++LENQ+ +P
Sbjct: 241 EGGLAKMRDSISNTAEYGDYTRGPRIVNEQTKAEMRKVLSEIQSGQFAREFVLENQSGKP 300

Query: 300 MFNAINRRELEHPIEVVGRKLRSMMPFIK 328
            F A+ R+E EHPIE VG+ LR+M  ++K
Sbjct: 301 GFTAMRRQEAEHPIEEVGKDLRAMFSWLK 329


Lambda     K      H
   0.320    0.138    0.404 

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: 389
Number of extensions: 13
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: 344
Length of database: 331
Length adjustment: 28
Effective length of query: 316
Effective length of database: 303
Effective search space:    95748
Effective search space used:    95748
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: 49 (23.5 bits)

Align candidate WP_011317028.1 AVA_RS00670 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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/TIGR00465.hmm
# target sequence database:        /tmp/gapView.840359.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-152  493.5   0.2   1.2e-152  493.3   0.2    1.0  1  NCBI__GCF_000204075.1:WP_011317028.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011317028.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.3   0.2  1.2e-152  1.2e-152       1     313 [.      15     328 ..      15     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 493.3 bits;  conditional E-value: 1.2e-152
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                           l+gk++aiiGyGsqG+a+alnl+dsglnvivgl+++++s +kA+  G+ v++v++a++ ad+imiLlpDevqk
  NCBI__GCF_000204075.1:WP_011317028.1  15 LAGKTIAIIGYGSQGHAHALNLKDSGLNVIVGLYPGSKSAEKAQAAGLTVKNVADAANVADFIMILLPDEVQK 87 
                                           689********************************************************************** PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           +vy++ei+p+l+eg++l f+HGfni+f q+v+p++vdvv+vAPKgpG+lvR++y++g+Gvp+l+Av+qd++g+
  NCBI__GCF_000204075.1:WP_011317028.1  88 TVYKNEIEPNLQEGNTLAFAHGFNIHFGQVVPPANVDVVMVAPKGPGHLVRRTYEQGQGVPALFAVYQDASGK 160
                                           ************************************************************************* PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           a++ Al+yAk+iGg+r gvlettF+eE+e+DLfGEqavLcGgl+alika+f+tLveaGyqpelAyfe++he+k
  NCBI__GCF_000204075.1:WP_011317028.1 161 ARDRALSYAKGIGGTRGGVLETTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPELAYFECLHEVK 233
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           livdl+ e+Gl++mrd++sntA++g+++++ +i++e++k+em+k+l eiq+G+fa+e++le++ gkp f+++r
  NCBI__GCF_000204075.1:WP_011317028.1 234 LIVDLVVEGGLAKMRDSISNTAEYGDYTRGpRIVNEQTKAEMRKVLSEIQSGQFAREFVLENQSGKPGFTAMR 306
                                           ************************************************************************* PP

                             TIGR00465 292 kkekeqeiekvGkelralvkae 313
                                           ++e e+ ie+vGk+lra++++ 
  NCBI__GCF_000204075.1:WP_011317028.1 307 RQEAEHPIEEVGKDLRAMFSWL 328
                                           *******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (331 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.55
//
[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