GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Marivita geojedonensis DPG-138

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_085636394.1 MGEO_RS09025 ketol-acid reductoisomerase

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



>NCBI__GCF_002115805.1:WP_085636394.1
          Length = 340

 Score =  456 bits (1174), Expect = e-133
 Identities = 225/340 (66%), Positives = 266/340 (78%), Gaps = 2/340 (0%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59
           M+V+YD+D D++LIK   V I+GYGSQGHAHALNL+DSG  NV V LR+  AS  KA   
Sbjct: 1   MRVYYDRDCDINLIKDMKVAILGYGSQGHAHALNLRDSGAKNVVVALREGSASAKKAEGE 60

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           GLQV  +AEA    D++M  +PDE  A+ YK  VHDN+KEGAA+AFAHG NVH+G + P+
Sbjct: 61  GLQVMGIAEAAAWCDLIMFTMPDELQAETYKKYVHDNLKEGAAIAFAHGLNVHFGLIEPK 120

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
             +DVIM+APK PGHTVR  YT+GGGVP L+AVH + SG A +I LSY +A GGGR+GII
Sbjct: 121 PGVDVIMMAPKGPGHTVRGEYTKGGGVPCLVAVHNDASGRALEIGLSYCSAIGGGRSGII 180

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ETNFREE ETDLFGEQAVLCGG VELI+ GFETLVEAGY PEMAYFECLHE+KLIVDLIY
Sbjct: 181 ETNFREECETDLFGEQAVLCGGLVELIRMGFETLVEAGYEPEMAYFECLHEVKLIVDLIY 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVT-EETKKAMKQCLTDIQTGEYAKSFLLENKAGA 298
           EGGIANMNYSISN AEYGEYV+GPR++  +ETK  MK  L+DIQTG++ + F+ EN  G 
Sbjct: 241 EGGIANMNYSISNTAEYGEYVSGPRILPYDETKARMKAVLSDIQTGKFVRDFMQENAVGQ 300

Query: 299 PTLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           P     RR+  EHQIE+VG  LR MMPWI+  KMVD+SKN
Sbjct: 301 PFFKGTRRINDEHQIEKVGETLRGMMPWISAGKMVDKSKN 340


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: 402
Number of extensions: 14
Number of successful extensions: 3
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: 340
Length adjustment: 28
Effective length of query: 310
Effective length of database: 312
Effective search space:    96720
Effective search space used:    96720
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_085636394.1 MGEO_RS09025 (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.857855.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-127  411.2   0.2   1.3e-127  411.0   0.2    1.0  1  NCBI__GCF_002115805.1:WP_085636394.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085636394.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.0   0.2  1.3e-127  1.3e-127       1     312 [.      14     328 ..      14     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 411.0 bits;  conditional E-value: 1.3e-127
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevq 72 
                                           +k+ kvai+GyGsqG+a+alnlrdsg  nv+v+lr+++as kkAe +G++v+ ++ea++  dlim  +pDe+q
  NCBI__GCF_002115805.1:WP_085636394.1  14 IKDMKVAILGYGSQGHAHALNLRDSGAkNVVVALREGSASAKKAEGEGLQVMGIAEAAAWCDLIMFTMPDELQ 86 
                                           6899**********************758******************************************** PP

                             TIGR00465  73 kevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtg 145
                                            e+y++ ++++lkeg+a+ f+HG n++f  i+++ +vdv+++APKgpG++vR ey +g Gvp l+Av++d++g
  NCBI__GCF_002115805.1:WP_085636394.1  87 AETYKKYVHDNLKEGAAIAFAHGLNVHFGLIEPKPGVDVIMMAPKGPGHTVRGEYTKGGGVPCLVAVHNDASG 159
                                           ************************************************************************* PP

                             TIGR00465 146 eakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhel 218
                                            a ei l+y  aiGg+r g++et F+eE+e+DLfGEqavLcGgl +li+++f+tLveaGy+pe+Ayfe++he+
  NCBI__GCF_002115805.1:WP_085636394.1 160 RALEIGLSYCSAIGGGRSGIIETNFREECETDLFGEQAVLCGGLVELIRMGFETLVEAGYEPEMAYFECLHEV 232
                                           ************************************************************************* PP

                             TIGR00465 219 klivdllkekGlelmrdavsntAklgalelr.eil.keelkkemqkilkeiqnGefakewalekeagkpafee 289
                                           klivdl++e+G+++m  ++sntA++g++ ++ +il  +e+k++m+ +l +iq+G+f ++++ e+++g+p f+ 
  NCBI__GCF_002115805.1:WP_085636394.1 233 KLIVDLIYEGGIANMNYSISNTAEYGEYVSGpRILpYDETKARMKAVLSDIQTGKFVRDFMQENAVGQPFFKG 305
                                           *******************************88874589********************************** PP

                             TIGR00465 290 arkkekeqeiekvGkelralvka 312
                                           +r+ + e++iekvG++lr ++++
  NCBI__GCF_002115805.1:WP_085636394.1 306 TRRINDEHQIEKVGETLRGMMPW 328
                                           *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (340 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: 15.87
//
[ok]

This GapMind analysis is from Jul 26 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