GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Xenophilus azovorans DSM 13620

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_038215898.1 Q392_RS26720 ketol-acid reductoisomerase

Query= metacyc::MONOMER-18814
         (338 letters)



>NCBI__GCF_000745855.1:WP_038215898.1
          Length = 338

 Score =  581 bits (1498), Expect = e-171
 Identities = 290/338 (85%), Positives = 306/338 (90%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60
           MKVFYDKD DLSLIKGK V IIGYGSQGHAHA NL DSGV V VGLRK GASW K   AG
Sbjct: 1   MKVFYDKDCDLSLIKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWPKVEKAG 60

Query: 61  LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120
           L+V EVAEAVK ADVVMILLPDEQIA VYKN+V  NIKEGA+L FAHGFNVHYG V PRA
Sbjct: 61  LKVAEVAEAVKQADVVMILLPDEQIASVYKNDVAPNIKEGASLVFAHGFNVHYGFVQPRA 120

Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180
           DLDV M+APKAPGHTVR+TYTQGGGVPHL+AVHQ+KSG ARD+ALSYA ANGGG+AGIIE
Sbjct: 121 DLDVWMVAPKAPGHTVRSTYTQGGGVPHLVAVHQDKSGKARDLALSYAMANGGGKAGIIE 180

Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240
           TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE
Sbjct: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300
           GGIANMNYSISNNAEYGEYVTGPR+VT+ETK  MK+ L DIQTGEYAKSF+LEN AGAPT
Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPRIVTDETKATMKKVLRDIQTGEYAKSFVLENAAGAPT 300

Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           LISRRRL AEHQIE VG KLRAMMPWI KNK+VDQ++N
Sbjct: 301 LISRRRLNAEHQIEVVGEKLRAMMPWIKKNKLVDQTRN 338


Lambda     K      H
   0.316    0.133    0.379 

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: 495
Number of extensions: 11
Number of successful extensions: 1
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_038215898.1 Q392_RS26720 (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.3780684.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-138  446.5   1.5   2.6e-138  446.2   1.5    1.0  1  NCBI__GCF_000745855.1:WP_038215898.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038215898.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.2   1.5  2.6e-138  2.6e-138       1     313 [.      14     327 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 446.2 bits;  conditional E-value: 2.6e-138
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                           +kgk+vaiiGyGsqG+a+a nl dsg++v+vglrk++asw k e+ G+kv +v+ea+k+ad++miLlpDe+  
  NCBI__GCF_000745855.1:WP_038215898.1  14 IKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWPKVEKAGLKVAEVAEAVKQADVVMILLPDEQIA 86 
                                           689********************************************************************** PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           +vy+++++p++keg++l+f+HGfn+++  +++++d+dv +vAPK+pG++vR++y +g Gvp+l+Av+qd +g+
  NCBI__GCF_000745855.1:WP_038215898.1  87 SVYKNDVAPNIKEGASLVFAHGFNVHYGFVQPRADLDVWMVAPKAPGHTVRSTYTQGGGVPHLVAVHQDKSGK 159
                                           ************************************************************************* PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           a++ Al+yA a Gg++ag++et F+eE+e+DLfGEqavLcGg  +lika+f+tLveaGy+pe+Ayfe++helk
  NCBI__GCF_000745855.1:WP_038215898.1 160 ARDLALSYAMANGGGKAGIIETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELK 232
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           livdl++e+G+++m  ++sn A++g++ ++ +i+++e+k++m+k+l +iq+Ge+ak ++le++ag+p++ + r
  NCBI__GCF_000745855.1:WP_038215898.1 233 LIVDLIYEGGIANMNYSISNNAEYGEYVTGpRIVTDETKATMKKVLRDIQTGEYAKSFVLENAAGAPTLISRR 305
                                           ******************************9****************************************** PP

                             TIGR00465 292 kkekeqeiekvGkelralvkae 313
                                           + + e++ie vG++lra++++ 
  NCBI__GCF_000745855.1:WP_038215898.1 306 RLNAEHQIEVVGEKLRAMMPWI 327
                                           *******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (338 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 13.16
//
[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