GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Dinoroseobacter shibae DFL-12

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate 3609007 Dshi_2396 ketol-acid reductoisomerase (RefSeq)

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



>FitnessBrowser__Dino:3609007
          Length = 340

 Score =  456 bits (1174), Expect = e-133
 Identities = 227/340 (66%), Positives = 267/340 (78%), Gaps = 2/340 (0%)

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

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           GLQV  +AEA    D++M  +PDE  A+ YK  VHDNI+EGAA+AFAHG NVH+G + P+
Sbjct: 61  GLQVMGIAEAAAWCDLIMFTMPDELQAETYKKYVHDNIREGAAIAFAHGLNVHFGLIEPK 120

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
           A +DVIM+APK PGHTVR  YT+GGGVP L+AV  + +G A +I LSY +A GGGR+GII
Sbjct: 121 AGVDVIMMAPKGPGHTVRGEYTKGGGVPCLVAVDTDATGRALEIGLSYCSAIGGGRSGII 180

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ETNFREE ETDLFGEQAVLCGG VELI+ GFETLVEAGYAPEMAYFECLHE+KLIVDLIY
Sbjct: 181 ETNFREECETDLFGEQAVLCGGLVELIRMGFETLVEAGYAPEMAYFECLHEVKLIVDLIY 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVT-EETKKAMKQCLTDIQTGEYAKSFLLENKAGA 298
           EGGIANMNYSISN AEYGEYV+GPRV+  +ETK  MK  LTDIQTG++ + F+ EN  G 
Sbjct: 241 EGGIANMNYSISNTAEYGEYVSGPRVLPYDETKARMKAILTDIQTGKFVRDFMQENTVGQ 300

Query: 299 PTLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           P     RRL  EHQIE VG +LR MMPWI+  K+VDQ KN
Sbjct: 301 PFFKGTRRLNDEHQIEAVGKELRGMMPWISAGKLVDQEKN 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: 409
Number of extensions: 16
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 3609007 Dshi_2396 (ketol-acid reductoisomerase (RefSeq))
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.22877.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.9e-127  408.3   0.2     1e-126  408.1   0.2    1.0  1  lcl|FitnessBrowser__Dino:3609007  Dshi_2396 ketol-acid reductoisom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609007  Dshi_2396 ketol-acid reductoisomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.1   0.2    1e-126    1e-126       1     312 [.      14     328 ..      14     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 408.1 bits;  conditional E-value: 1e-126
                         TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkevy 76 
                                       +k+kkvai+GyGsqG+a+alnlrdsg  n++v+lr+++as kkAe +G++v+ ++ea++  dlim  +pDe+q e+y
  lcl|FitnessBrowser__Dino:3609007  14 IKDKKVAILGYGSQGHAHALNLRDSGAkNLVVALREGSASAKKAEAEGLQVMGIAEAAAWCDLIMFTMPDELQAETY 90 
                                       689***********************75799********************************************** PP

                         TIGR00465  77 eaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakeiAla 153
                                       ++ ++++++eg+a+ f+HG n++f  i+++++vdv+++APKgpG++vR ey +g Gvp l+Av +d+tg a ei l+
  lcl|FitnessBrowser__Dino:3609007  91 KKYVHDNIREGAAIAFAHGLNVHFGLIEPKAGVDVIMMAPKGPGHTVRGEYTKGGGVPCLVAVDTDATGRALEIGLS 167
                                       ***************************************************************************** PP

                         TIGR00465 154 yAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGl 230
                                       y  aiGg+r g++et F+eE+e+DLfGEqavLcGgl +li+++f+tLveaGy+pe+Ayfe++he+klivdl++e+G+
  lcl|FitnessBrowser__Dino:3609007 168 YCSAIGGGRSGIIETNFREECETDLFGEQAVLCGGLVELIRMGFETLVEAGYAPEMAYFECLHEVKLIVDLIYEGGI 244
                                       ***************************************************************************** PP

                         TIGR00465 231 elmrdavsntAklgalelr.eil.keelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGke 305
                                       ++m  ++sntA++g++ ++ ++l  +e+k++m+ il +iq+G+f ++++ e+++g+p f+ +r+ + e++ie vGke
  lcl|FitnessBrowser__Dino:3609007 245 ANMNYSISNTAEYGEYVSGpRVLpYDETKARMKAILTDIQTGKFVRDFMQENTVGQPFFKGTRRLNDEHQIEAVGKE 321
                                       *******************87774589************************************************** PP

                         TIGR00465 306 lralvka 312
                                       lr ++++
  lcl|FitnessBrowser__Dino:3609007 322 LRGMMPW 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 11.94
//
[ok]

This GapMind analysis is from Apr 09 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:

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