Alignments for a candidate for ilvC in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Desulfobulbus mediterraneus DSM 13871

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate WP_028585882.1 G494_RS0119665 ketol-acid reductoisomerase

Query= BRENDA::A0KS29
         (492 letters)



>NCBI__GCF_000429965.1:WP_028585882.1
          Length = 490

 Score =  725 bits (1872), Expect = 0.0
 Identities = 356/488 (72%), Positives = 415/488 (85%), Gaps = 1/488 (0%)

Query: 3   NYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSGLN 62
           NYFN+L LR QL +LG+CRFMD SEF DG + +K   IVI+GCGAQGL+QGLN+RDSGL+
Sbjct: 4   NYFNTLPLRLQLEELGKCRFMDASEF-DGVDALKGKKIVIVGCGAQGLHQGLNLRDSGLD 62

Query: 63  IAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMPLM 122
           ++YALR  AI++KR SW+ A++NGF V  +E LIP ADLV+NLTPDKQH+NVVSAVMPLM
Sbjct: 63  VSYALRDSAISEKRQSWKNASENGFVVDNYEALIPGADLVINLTPDKQHTNVVSAVMPLM 122

Query: 123 KQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPEND 182
           KQGA LSYSHGFNIVEEGM+IR D+TV+MVAPK PGTEVREEYKRGFGVPTLIAVH END
Sbjct: 123 KQGACLSYSHGFNIVEEGMKIREDLTVIMVAPKSPGTEVREEYKRGFGVPTLIAVHREND 182

Query: 183 PNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKMVA 242
           P   G  +AKAYA+ TGGDRAGVLQSSF+AEVKSDLMGEQTILCGMLQ G++L +DKM+A
Sbjct: 183 PQEQGWALAKAYAAGTGGDRAGVLQSSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKMIA 242

Query: 243 DGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLFEK 302
            G+EPGYA+KL+Q GWETVTEALKHGGITNMMDRLSNPAKIKAF +AE+L+EIL PLFEK
Sbjct: 243 QGIEPGYASKLVQYGWETVTEALKHGGITNMMDRLSNPAKIKAFYLAEELREILTPLFEK 302

Query: 303 HMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIFLV 362
           HMDDI+SG FS TMM DW NDD NLL WRAETAE+ FE +  +   I EQ YFD GI +V
Sbjct: 303 HMDDIMSGHFSSTMMADWDNDDLNLLTWRAETAESAFEKSQSTDAEIAEQAYFDNGILMV 362

Query: 363 AMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYGCY 422
           AM+KAGVELAF+TMV+AGI EESAYYESLHE PLIANTIARK+LYEMNVVISDTAEYGCY
Sbjct: 363 AMVKAGVELAFETMVAAGIKEESAYYESLHEVPLIANTIARKKLYEMNVVISDTAEYGCY 422

Query: 423 LFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELRGY 482
           LF H AVPML +++  ++ + +G GL+ S N VDN++LI +N+AIR+T VE +G ELR Y
Sbjct: 423 LFAHQAVPMLAEFMTKVNSDVIGKGLETSDNGVDNIELIKVNEAIRYTPVELVGEELRSY 482

Query: 483 MTDMKSIV 490
           M  MK I+
Sbjct: 483 MGAMKPII 490


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: 825
Number of extensions: 22
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: 492
Length of database: 490
Length adjustment: 34
Effective length of query: 458
Effective length of database: 456
Effective search space:   208848
Effective search space used:   208848
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_028585882.1 G494_RS0119665 (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.8973.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-134  432.7   0.9     4e-121  389.8   0.1    2.0  2  lcl|NCBI__GCF_000429965.1:WP_028585882.1  G494_RS0119665 ketol-acid reduct


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028585882.1  G494_RS0119665 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.8   0.1    4e-121    4e-121       1     312 [.      35     367 ..      35     369 .. 0.97
   2 !   47.8   0.2     5e-17     5e-17     185     312 ..     361     485 ..     359     487 .. 0.88

  Alignments for each domain:
  == domain 1  score: 389.8 bits;  conditional E-value: 4e-121
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlim 64 
                                               lkgkk++i+G+G+qG  q+lnlrdsgl+v+++lr +a     +swk+A+e+Gf v ++e +i+ adl++
  lcl|NCBI__GCF_000429965.1:WP_028585882.1  35 LKGKKIVIVGCGAQGLHQGLNLRDSGLDVSYALRDSAisekrQSWKNASENGFVVDNYEALIPGADLVI 103
                                               79*********************************9999999*************************** PP

                                 TIGR00465  65 iLlpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGv 133
                                               +L+pD+ q+++++  ++pl+k+g+ l++sHGfniv+++++i++d++v++vAPK+pG++vReeyk+g+Gv
  lcl|NCBI__GCF_000429965.1:WP_028585882.1 104 NLTPDK-QHTNVVSAVMPLMKQGACLSYSHGFNIVEEGMKIREDLTVIMVAPKSPGTEVREEYKRGFGV 171
                                               ******.77777777****************************************************** PP

                                 TIGR00465 134 psliAveqd..vtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtL 200
                                               p+liAv+++  ++ ++ + A+ayA+++Gg ragvl+++F++Ev+sDL+GEq++LcG+l+a+++++fd++
  lcl|NCBI__GCF_000429965.1:WP_028585882.1 172 PTLIAVHREndPQEQGWALAKAYAAGTGGDRAGVLQSSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKM 240
                                               ******9987799******************************************************** PP

                                 TIGR00465 201 veaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqn 269
                                               +++G +p +A +++++++++++++lk++G+++m+d++sn+Ak++a+ l+e l+e l + ++k++++i +
  lcl|NCBI__GCF_000429965.1:WP_028585882.1 241 IAQGIEPGYASKLVQYGWETVTEALKHGGITNMMDRLSNPAKIKAFYLAEELREILTPLFEKHMDDIMS 309
                                               ********************************************************************* PP

                                 TIGR00465 270 Gefak....ewalek........eagkpafeearkke...keqeiekvGkelralvka 312
                                               G+f++    +w +++        e++++afe+ + ++    eq ++++G  + a+vka
  lcl|NCBI__GCF_000429965.1:WP_028585882.1 310 GHFSStmmaDWDNDDlnlltwraETAESAFEKSQSTDaeiAEQAYFDNGILMVAMVKA 367
                                               ****99999999999******99999*****99999888999**************97 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 5e-17
                                 TIGR00465 185 LcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilk 253
                                               ++ +++a++++af+t+v+aG ++e Ay e +he+ li++ + +k l +m   +s+tA++g +  +++  
  lcl|NCBI__GCF_000429965.1:WP_028585882.1 361 MVAMVKAGVELAFETMVAAGIKEESAYYESLHEVPLIANTIARKKLYEMNVVISDTAEYGCYLFAHQAV 429
                                               5689*************************************************************9999 PP

                                 TIGR00465 254 eelkkemqkilke.iqnGefakewalekeagkpafeearkkekeqeiekvGkelralvka 312
                                                 l++ m+k+  + i +G ++++  +++     ++ + +++ + + +e vG+elr  + a
  lcl|NCBI__GCF_000429965.1:WP_028585882.1 430 PMLAEFMTKVNSDvIGKGLETSDNGVDN----IELIKVNEAIRYTPVELVGEELRSYMGA 485
                                               9999999999877255899999776666....6777777777888999999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (490 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 3.12
//
[ok]

This GapMind analysis is from Apr 10 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