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

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.4094.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 12.25
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis