Alignments for a candidate for ilvC in Desulfallas geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Desulfallas geothermicus DSM 3669

Align Ketol-acid reductoisomerase (NAD(P)(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.383 (characterized)
to candidate WP_092483008.1 BM299_RS08295 ketol-acid reductoisomerase

Query= SwissProt::Q0AV19
         (337 letters)



>NCBI__GCF_900115975.1:WP_092483008.1
          Length = 331

 Score =  481 bits (1238), Expect = e-140
 Identities = 240/335 (71%), Positives = 278/335 (82%), Gaps = 5/335 (1%)

Query: 1   MARMFYDADANLENLKGKTIAVMGFGSQGHAQAQNLKESGLNVIVGLRKPFDEASEKEWN 60
           M ++FYD DA+L  LKGK IAVMGFGSQGHAQ+QNLKESGL+V+VGLRK  D AS   W 
Sbjct: 1   MVKVFYDQDADLAVLKGKKIAVMGFGSQGHAQSQNLKESGLDVVVGLRK--DSAS---WA 55

Query: 61  AVIAAGITPMSVAEAAEAADVIQILLPDEVQARVYNAEIKPYLKAGNALGFSHGFNIHFG 120
              AAG+   +VAEAA  AD+IQILLPDE QARVY  EI+PYL  G AL FSHGFNIHFG
Sbjct: 56  RAEAAGLQVATVAEAAGQADIIQILLPDEYQARVYKEEIEPYLTEGKALMFSHGFNIHFG 115

Query: 121 QIVPPAFVDVFMVAPKSPGHLVRRMYVKGAGVPGLVAVQQDYSGKAKDLALAYACGIGCT 180
           QIVPP  VDVF+VAPKSPGHLVRRMYV G GVPGLVAV QDY+G+A+D+ +AYA GIGCT
Sbjct: 116 QIVPPNNVDVFLVAPKSPGHLVRRMYVDGQGVPGLVAVHQDYTGRARDITMAYAKGIGCT 175

Query: 181 RAGVIETSFQEETETDLFGEQCVLCGGVTELVKAGFETLVEAGYQPEIAYFECMHELKLI 240
           RAGV ET+F EETETDLFGEQCVLCGGV+EL+KAGFETLVEAGY PE+AYFEC+HELKLI
Sbjct: 176 RAGVFETTFAEETETDLFGEQCVLCGGVSELIKAGFETLVEAGYAPEMAYFECLHELKLI 235

Query: 241 VDLMYEGGMSYMRYSISDTAEWGDYTKGPEIIGEEARYAMYEALQDIQDGSFAKGWLLEN 300
           VDL+ EGG+++MR+SIS+TAE+GDY  GP II E+ R  M   LQ+IQDG FAK W+LEN
Sbjct: 236 VDLINEGGLTWMRHSISNTAEYGDYITGPRIINEDTREEMRAVLQEIQDGVFAKEWILEN 295

Query: 301 MVGRPRFNALKRQNREHLIEEVGAELRGMMPWLKE 335
              RP +NA+K++ +EH IE+VGAELR MMPWLK+
Sbjct: 296 QANRPVYNAIKKREQEHPIEQVGAELRQMMPWLKK 330


Lambda     K      H
   0.319    0.136    0.404 

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: 421
Number of extensions: 14
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: 337
Length of database: 331
Length adjustment: 28
Effective length of query: 309
Effective length of database: 303
Effective search space:    93627
Effective search space used:    93627
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_092483008.1 BM299_RS08295 (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.10866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-147  476.8   0.1   1.5e-147  476.6   0.1    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092483008.1  BM299_RS08295 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092483008.1  BM299_RS08295 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.6   0.1  1.5e-147  1.5e-147       1     314 []      15     329 ..      15     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 476.6 bits;  conditional E-value: 1.5e-147
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 
                                               lkgkk+a++G+GsqG+aq+ nl++sgl+v+vglrk++asw++Ae  G++v tv+ea+ +ad+i iLlpD
  lcl|NCBI__GCF_900115975.1:WP_092483008.1  15 LKGKKIAVMGFGSQGHAQSQNLKESGLDVVVGLRKDSASWARAEAAGLQVATVAEAAGQADIIQILLPD 83 
                                               79******************************************************************* PP

                                 TIGR00465  70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138
                                               e q +vy++ei+p+l+egkal+fsHGfni+f qiv+p++vdv+lvAPK+pG+lvR++y  g+Gvp+l+A
  lcl|NCBI__GCF_900115975.1:WP_092483008.1  84 EYQARVYKEEIEPYLTEGKALMFSHGFNIHFGQIVPPNNVDVFLVAPKSPGHLVRRMYVDGQGVPGLVA 152
                                               ********************************************************************* PP

                                 TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207
                                               v+qd+tg a++i +ayAk+iG +ragv+ettF eE+e+DLfGEq vLcGg+++lika+f+tLveaGy+p
  lcl|NCBI__GCF_900115975.1:WP_092483008.1 153 VHQDYTGRARDITMAYAKGIGCTRAGVFETTFAEETETDLFGEQCVLCGGVSELIKAGFETLVEAGYAP 221
                                               ********************************************************************* PP

                                 TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275
                                               e+Ayfe++helklivdl++e+Gl+ mr+++sntA++g++ ++ +i++e +++em+ +l+eiq+G fake
  lcl|NCBI__GCF_900115975.1:WP_092483008.1 222 EMAYFECLHELKLIVDLINEGGLTWMRHSISNTAEYGDYITGpRIINEDTREEMRAVLQEIQDGVFAKE 290
                                               ****************************************999************************** PP

                                 TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkaek 314
                                               w+le++a++p +++++k+e+e+ ie+vG elr+++++ k
  lcl|NCBI__GCF_900115975.1:WP_092483008.1 291 WILENQANRPVYNAIKKREQEHPIEQVGAELRQMMPWLK 329
                                               ***********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (331 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: 00:00:00.01
# Mc/sec: 7.74
//
[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