Alignments for a candidate for ilvC in Oleispira antarctica

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Oleispira antarctica

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate WP_046007847.1 OLEAN_RS02055 ketol-acid reductoisomerase

Query= BRENDA::A0KS29
         (492 letters)



>NCBI__GCF_000967895.1:WP_046007847.1
          Length = 496

 Score =  752 bits (1941), Expect = 0.0
 Identities = 366/491 (74%), Positives = 434/491 (88%), Gaps = 1/491 (0%)

Query: 3   NYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSGLN 62
           NYFN+LNLR+QL QLG+CRFM+RSEF+DGC  +K   IVI+GCGAQGLNQGLNMRDSGL+
Sbjct: 4   NYFNTLNLREQLDQLGRCRFMNRSEFADGCEALKGKKIVIVGCGAQGLNQGLNMRDSGLD 63

Query: 63  IAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMPLM 122
           I+Y LR  AIA+KRAS+  A++NGF VGT+E+LIP ADLVLNLTPDKQH+ VV+A+MPLM
Sbjct: 64  ISYTLRAAAIAEKRASFVNASENGFVVGTYEDLIPQADLVLNLTPDKQHTAVVTAIMPLM 123

Query: 123 KQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPEND 182
           K+ +TL+YSHGFN+VEEGM+IR DITV+MVAPKCPG+EVREEYKRGFGVPTL+AVHPEND
Sbjct: 124 KKNSTLAYSHGFNVVEEGMKIREDITVIMVAPKCPGSEVREEYKRGFGVPTLLAVHPEND 183

Query: 183 PNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKMVA 242
           P G+G ++AKAYASATGGDRAG L+SSF+AEVKSDLMGEQTILCGMLQTGAILGY+KMVA
Sbjct: 184 PRGEGWDLAKAYASATGGDRAGCLESSFVAEVKSDLMGEQTILCGMLQTGAILGYEKMVA 243

Query: 243 DGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLFEK 302
           DG++  YAAKLIQ GWETVTEALK GGITNMMDRL+NPAKI AF++AE+LK++++PLF K
Sbjct: 244 DGIDGPYAAKLIQFGWETVTEALKIGGITNMMDRLANPAKIVAFDMAEELKDLMRPLFRK 303

Query: 303 HMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIFLV 362
           H DDII+G FS+TMM+DWANDD NLL+WR ETAETGFE A  +   IDEQ +FDKGI LV
Sbjct: 304 HQDDIITGHFSKTMMEDWANDDVNLLKWREETAETGFEKAAPTDAVIDEQEFFDKGIMLV 363

Query: 363 AMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYGCY 422
           AM+KAGVELAF++MV +GIVEESAYYESLHETPLIANTIARK+LYEMNVVISDTAEYGCY
Sbjct: 364 AMVKAGVELAFESMVESGIVEESAYYESLHETPLIANTIARKKLYEMNVVISDTAEYGCY 423

Query: 423 LFNHAAVPMLRD-YVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELRG 481
           LF HAA+P+L + ++  ++ E +G GL  +S +VDN +L+ +ND IR+  VEY+G ELRG
Sbjct: 424 LFAHAAIPLLAEKFMPNITTEVIGKGLNLTSTSVDNARLVEVNDEIRNHPVEYVGEELRG 483

Query: 482 YMTDMKSIVGA 492
           YMTDMK IV A
Sbjct: 484 YMTDMKRIVEA 494


Lambda     K      H
   0.317    0.134    0.389 

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: 803
Number of extensions: 18
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: 492
Length of database: 496
Length adjustment: 34
Effective length of query: 458
Effective length of database: 462
Effective search space:   211596
Effective search space used:   211596
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_046007847.1 OLEAN_RS02055 (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.24653.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-130  419.9   0.4   6.4e-119  382.5   0.1    2.0  2  lcl|NCBI__GCF_000967895.1:WP_046007847.1  OLEAN_RS02055 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000967895.1:WP_046007847.1  OLEAN_RS02055 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.5   0.1  6.4e-119  6.4e-119       1     312 [.      36     368 ..      36     370 .. 0.97
   2 !   43.8   0.1   8.1e-16   8.1e-16     182     311 ..     359     486 ..     352     489 .. 0.84

  Alignments for each domain:
  == domain 1  score: 382.5 bits;  conditional E-value: 6.4e-119
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlim 64 
                                               lkgkk++i+G+G+qG +q+ln+rdsgl+++++lr  a     as+ +A+e+Gf v t+e++i++adl++
  lcl|NCBI__GCF_000967895.1:WP_046007847.1  36 LKGKKIVIVGCGAQGLNQGLNMRDSGLDISYTLRAAAiaekrASFVNASENGFVVGTYEDLIPQADLVL 104
                                               79********************************99999999*************************** PP

                                 TIGR00465  65 iLlpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGv 133
                                               +L+pD+ q++ ++  i+pl+k++++l +sHGfn+v+++++i++d++v++vAPK+pG++vReeyk+g+Gv
  lcl|NCBI__GCF_000967895.1:WP_046007847.1 105 NLTPDK-QHTAVVTAIMPLMKKNSTLAYSHGFNVVEEGMKIREDITVIMVAPKCPGSEVREEYKRGFGV 172
                                               ******.77777777****************************************************** PP

                                 TIGR00465 134 psliAveqd..vtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtL 200
                                               p+l+Av+++  + ge+ + A+ayA a+Gg rag le++F++Ev+sDL+GEq++LcG+l+ +  ++++++
  lcl|NCBI__GCF_000967895.1:WP_046007847.1 173 PTLLAVHPEndPRGEGWDLAKAYASATGGDRAGCLESSFVAEVKSDLMGEQTILCGMLQTGAILGYEKM 241
                                               ******988779********************************************************* PP

                                 TIGR00465 201 veaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqn 269
                                               v++G +  +A ++i++++++++++lk +G+++m+d+++n+Ak+ a++++e lk+ +++ ++k+ ++i++
  lcl|NCBI__GCF_000967895.1:WP_046007847.1 242 VADGIDGPYAAKLIQFGWETVTEALKIGGITNMMDRLANPAKIVAFDMAEELKDLMRPLFRKHQDDIIT 310
                                               ********************************************************************* PP

                                 TIGR00465 270 Gefak....ewalek........eagkpafeearkke...keqeiekvGkelralvka 312
                                               G+f+k    +wa+++        e++++ fe+a  ++    eqe++++G  l a+vka
  lcl|NCBI__GCF_000967895.1:WP_046007847.1 311 GHFSKtmmeDWANDDvnllkwreETAETGFEKAAPTDaviDEQEFFDKGIMLVAMVKA 368
                                               *****99999****9*******9999*****999999999***************997 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 8.1e-16
                                 TIGR00465 182 qavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr. 249
                                                 +L+ +++a++++af+ +ve G  +e Ay e +he  li++ + +k l +m   +s+tA++g +  + 
  lcl|NCBI__GCF_000967895.1:WP_046007847.1 359 GIMLVAMVKAGVELAFESMVESGIVEESAYYESLHETPLIANTIARKKLYEMNVVISDTAEYGCYLFAh 427
                                               56899***********************************************************99886 PP

                                 TIGR00465 250 eilkeelkkemqkilkeiq.nGefakewalekeagkpafeearkkekeqeiekvGkelralvk 311
                                                 +    +k m +i  e++ +G         ++++++++ e +   +++ +e vG+elr  + 
  lcl|NCBI__GCF_000967895.1:WP_046007847.1 428 AAIPLLAEKFMPNITTEVIgKGLNLT----STSVDNARLVEVNDEIRNHPVEYVGEELRGYMT 486
                                               77777778888888777651343333....4456668999999999************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (496 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 3.75
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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