Alignments for a candidate for ilvC in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Thermocrinis albus DSM 14484

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_041434214.1 THAL_RS04555 ketol-acid reductoisomerase

Query= SwissProt::B4U6I9
         (333 letters)



>NCBI__GCF_000025605.1:WP_041434214.1
          Length = 333

 Score =  545 bits (1405), Expect = e-160
 Identities = 263/333 (78%), Positives = 295/333 (88%)

Query: 1   MAKIYYDEDASLGILAMKTVAIVGYGSQGHAHALNLRDSGIRVIVALDDKSPHRKTAMED 60
           MAK+YYD DA+L  L  KTVAI+GYGSQGHAHALNLRDSGIRV++ L   S  R  A++D
Sbjct: 1   MAKVYYDADATLEPLIGKTVAILGYGSQGHAHALNLRDSGIRVVIGLPAGSKSRTKALQD 60

Query: 61  GFSVYTTSRATQEADVIMILTPDTVQPAVYKECIEPNLTPGKAIAFAHGFNIHFGQIVPP 120
           GF VY  +RA QEAD++M+LTPDTVQP +YKE +EP L   K++AFAHGFNIHF QIVPP
Sbjct: 61  GFPVYEPARAVQEADIVMMLTPDTVQPQLYKESVEPYLDSSKSLAFAHGFNIHFRQIVPP 120

Query: 121 KDIDVFMVAPKGPGHLVRWMYEEGKGVPALISIHQDATGSCRDIALAYAKGIGATRAGVI 180
             +DVFMVAPKGPGHLVRWMYEEGKGVPALI+IHQDATG+CRD ALAYAK IGATRAGVI
Sbjct: 121 PSVDVFMVAPKGPGHLVRWMYEEGKGVPALIAIHQDATGTCRDKALAYAKAIGATRAGVI 180

Query: 181 ETTFREETETDLFGEQAVLCGGATALIKAGFETLVEAGYQPEMAYFECLHELKLIVDLIY 240
           ETTF+EETETDLFGEQAVLCGG TALIKAGFETLVEAGYQPE+AYFECLHELKLIVDLIY
Sbjct: 181 ETTFKEETETDLFGEQAVLCGGVTALIKAGFETLVEAGYQPEVAYFECLHELKLIVDLIY 240

Query: 241 QHGIAGMRYSISDTAKYGDVTRGDRVYEAVKPLMKQMLKEIQDGEFAREWILENQANRPV 300
           Q+GI+GMRYSISDTAKYGDVTRG R+YE VKPLMK++L+EIQ GEFAREW+LENQA RPV
Sbjct: 241 QYGISGMRYSISDTAKYGDVTRGRRIYEVVKPLMKKILEEIQTGEFAREWVLENQAGRPV 300

Query: 301 YNALLNKDKEHLVEKVGKELRQMMPWLSGKELK 333
           ++ALL KDKEH +EKVG +LR MMPWL GK+LK
Sbjct: 301 FHALLEKDKEHTIEKVGSQLRNMMPWLGGKDLK 333


Lambda     K      H
   0.319    0.136    0.402 

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: 456
Number of extensions: 8
Number of successful extensions: 1
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: 333
Length of database: 333
Length adjustment: 28
Effective length of query: 305
Effective length of database: 305
Effective search space:    93025
Effective search space used:    93025
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_041434214.1 THAL_RS04555 (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.664354.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-144  467.1   0.0   1.3e-144  466.9   0.0    1.0  1  NCBI__GCF_000025605.1:WP_041434214.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025605.1:WP_041434214.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.9   0.0  1.3e-144  1.3e-144       2     312 ..      16     326 ..      15     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 466.9 bits;  conditional E-value: 1.3e-144
                             TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqke 74 
                                            gk+vai+GyGsqG+a+alnlrdsg+ v++gl  +++s +kA +dGf v + + a+++ad++m+L+pD+vq++
  NCBI__GCF_000025605.1:WP_041434214.1  16 IGKTVAILGYGSQGHAHALNLRDSGIRVVIGLPAGSKSRTKALQDGFPVYEPARAVQEADIVMMLTPDTVQPQ 88 
                                           589********************************************************************** PP

                             TIGR00465  75 vyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgea 147
                                            y+++++p+l   k+l f+HGfni+f+qiv+p  vdv++vAPKgpG+lvR +y+eg+Gvp+liA++qd+tg  
  NCBI__GCF_000025605.1:WP_041434214.1  89 LYKESVEPYLDSSKSLAFAHGFNIHFRQIVPPPSVDVFMVAPKGPGHLVRWMYEEGKGVPALIAIHQDATGTC 161
                                           ************************************************************************* PP

                             TIGR00465 148 keiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelkl 220
                                           +++AlayAkaiG++ragv+ettFkeE+e+DLfGEqavLcGg++alika+f+tLveaGyqpe+Ayfe++helkl
  NCBI__GCF_000025605.1:WP_041434214.1 162 RDKALAYAKAIGATRAGVIETTFKEETETDLFGEQAVLCGGVTALIKAGFETLVEAGYQPEVAYFECLHELKL 234
                                           ************************************************************************* PP

                             TIGR00465 221 ivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakewalekeagkpafeearkk 293
                                           ivdl++++G+++mr ++s+tAk+g++++++ + e +k+ m+kil+eiq+Gefa+ew+le++ag+p f++  +k
  NCBI__GCF_000025605.1:WP_041434214.1 235 IVDLIYQYGISGMRYSISDTAKYGDVTRGRRIYEVVKPLMKKILEEIQTGEFAREWVLENQAGRPVFHALLEK 307
                                           ************************************************************************* PP

                             TIGR00465 294 ekeqeiekvGkelralvka 312
                                           +ke+ iekvG++lr+++++
  NCBI__GCF_000025605.1:WP_041434214.1 308 DKEHTIEKVGSQLRNMMPW 326
                                           *****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (333 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: 14.01
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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