Alignments for a candidate for ilvC in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Arcobacter nitrofigilis DSM 7299

Align Ketol-acid reductoisomerase (NADP(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.86 (characterized)
to candidate WP_013136629.1 ARNIT_RS14250 ketol-acid reductoisomerase

Query= SwissProt::Q9HVA2
         (338 letters)



>NCBI__GCF_000092245.1:WP_013136629.1
          Length = 340

 Score =  470 bits (1210), Expect = e-137
 Identities = 232/338 (68%), Positives = 270/338 (79%)

Query: 1   MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSATVAKAEAHG 60
           + V+YDKDC++ +I+ KKVA+IG+GSQGHAHA NL+DSGV+V VGLR G ++  KAEA G
Sbjct: 3   INVYYDKDCNIELIKSKKVAMIGFGSQGHAHAENLRDSGVEVVVGLRKGGSSWTKAEAKG 62

Query: 61  LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120
             V  V  A   ADVVMIL PDE Q  +Y  EI+PNLK GA LAF HGF+IHY +++P A
Sbjct: 63  FVVKTVAEATTGADVVMILLPDENQSEIYYSEIKPNLKDGAYLAFGHGFNIHYGRIIPDA 122

Query: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGIIE 180
             +V+M+APKAPGHTVRSEF KGGGIPDLIA+  + SG+ K VAL+YA  +GGGRTGIIE
Sbjct: 123 KTNVMMVAPKAPGHTVRSEFTKGGGIPDLIAVETNPSGDTKEVALAYASAIGGGRTGIIE 182

Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240
           TTFKDETETDLFGEQAVLCGG V LV+AGFETL EAGY PEMAYFECLHELKLIVDLMYE
Sbjct: 183 TTFKDETETDLFGEQAVLCGGAVSLVQAGFETLTEAGYEPEMAYFECLHELKLIVDLMYE 242

Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYPS 300
           GGI++M YSISN AEYG+YV+G  VINAES+AAM+  LK IQDG +AK FI EG A YP 
Sbjct: 243 GGISDMRYSISNTAEYGDYVSGKRVINAESKAAMKEILKEIQDGRFAKDFILEGQAGYPR 302

Query: 301 MTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338
           M A R N  A  IEQ G KLR MMPWI+++KIVD +KN
Sbjct: 303 MNAERANAKASLIEQTGNKLRKMMPWISSSKIVDLNKN 340


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: 406
Number of extensions: 3
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: 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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_013136629.1 ARNIT_RS14250 (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.1698.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-135  436.4   1.2     3e-135  436.2   1.2    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013136629.1  ARNIT_RS14250 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013136629.1  ARNIT_RS14250 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.2   1.2    3e-135    3e-135       1     312 [.      16     328 ..      16     330 .. 0.99

  Alignments for each domain:
  == domain 1  score: 436.2 bits;  conditional E-value: 3e-135
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 
                                               +k+kkva+iG+GsqG+a+a nlrdsg++v+vglrk+++sw+kAe +Gf v+tv+ea + ad++miLlpD
  lcl|NCBI__GCF_000092245.1:WP_013136629.1  16 IKSKKVAMIGFGSQGHAHAENLRDSGVEVVVGLRKGGSSWTKAEAKGFVVKTVAEATTGADVVMILLPD 84 
                                               689****************************************************************** PP

                                 TIGR00465  70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138
                                               e q+e y  eikp+lk+g+ l f HGfni++ +i + ++ +v++vAPK+pG++vR+e+ +g G+p liA
  lcl|NCBI__GCF_000092245.1:WP_013136629.1  85 ENQSEIYYSEIKPNLKDGAYLAFGHGFNIHYGRIIPDAKTNVMMVAPKAPGHTVRSEFTKGGGIPDLIA 153
                                               ********************************************************************* PP

                                 TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207
                                               ve++++g++ke+AlayA aiGg+r g++ettFk+E+e+DLfGEqavLcGg   l++a+f+tL+eaGy+p
  lcl|NCBI__GCF_000092245.1:WP_013136629.1 154 VETNPSGDTKEVALAYASAIGGGRTGIIETTFKDETETDLFGEQAVLCGGAVSLVQAGFETLTEAGYEP 222
                                               ********************************************************************* PP

                                 TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275
                                               e+Ayfe++helklivdl++e+G++ mr ++sntA++g++ ++ +++++e k++m++ilkeiq+G+fak+
  lcl|NCBI__GCF_000092245.1:WP_013136629.1 223 EMAYFECLHELKLIVDLMYEGGISDMRYSISNTAEYGDYVSGkRVINAESKAAMKEILKEIQDGRFAKD 291
                                               *****************************************99************************** PP

                                 TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312
                                               ++le +ag+p+++++r   k   ie++G++lr+++++
  lcl|NCBI__GCF_000092245.1:WP_013136629.1 292 FILEGQAGYPRMNAERANAKASLIEQTGNKLRKMMPW 328
                                               ***********************************98 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: 00:00:00.01
# Mc/sec: 9.18
//
[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