Alignments for a candidate for ilvC in Novosphingobium aromaticivorans DSM 12444

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Novosphingobium aromaticivorans DSM 12444

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_083760869.1 SARO_RS11385 ketol-acid reductoisomerase

Query= metacyc::MONOMER-18814
         (338 letters)



>NCBI__GCF_000013325.1:WP_083760869.1
          Length = 355

 Score =  464 bits (1195), Expect = e-135
 Identities = 229/339 (67%), Positives = 269/339 (79%), Gaps = 1/339 (0%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59
           MKV+YD D DL+LI  K + I+GYGSQGHAHA NL+DSGV +V + LR   AS  KA  A
Sbjct: 17  MKVYYDADCDLNLITDKKIAILGYGSQGHAHAQNLRDSGVKDVAIALRPGSASAKKAEAA 76

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           G +V   A+A   AD++MIL PDE  A +Y +++H N+K GAALAFAHG N+H+G +  R
Sbjct: 77  GFKVLANADAAAWADILMILAPDEHQAAIYADDLHANMKPGAALAFAHGLNIHFGLIEAR 136

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
           AD+DVIMIAPK PGHTVR+ Y +GGGVP LIAVHQN +G A D+AL+YA+  GGGR+GII
Sbjct: 137 ADIDVIMIAPKGPGHTVRSEYQRGGGVPCLIAVHQNVTGNAHDVALAYASGVGGGRSGII 196

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ETNFREE ETDLFGEQ VLCGGT  LI+AGFETLVEAGYAPEMAYFECLHELKLIVDL+Y
Sbjct: 197 ETNFREECETDLFGEQVVLCGGTTALIQAGFETLVEAGYAPEMAYFECLHELKLIVDLLY 256

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299
           EGGIANM YSISN AEYG+  TGPR++TEETKK MK+ L DIQ G + K F+L+N+AG P
Sbjct: 257 EGGIANMRYSISNTAEYGDIKTGPRIITEETKKEMKRVLADIQEGRFVKDFVLDNRAGQP 316

Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
            L + R L   HQIEE GAKLRAMMPWI  NK+VDQ+KN
Sbjct: 317 ELKAARGLAKRHQIEETGAKLRAMMPWIGANKLVDQTKN 355


Lambda     K      H
   0.316    0.133    0.379 

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: 463
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: 338
Length of database: 355
Length adjustment: 29
Effective length of query: 309
Effective length of database: 326
Effective search space:   100734
Effective search space used:   100734
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_083760869.1 SARO_RS11385 (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.877411.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-133  430.4   0.3     2e-133  430.1   0.3    1.0  1  NCBI__GCF_000013325.1:WP_083760869.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013325.1:WP_083760869.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.1   0.3    2e-133    2e-133       2     312 ..      31     343 ..      30     345 .. 0.99

  Alignments for each domain:
  == domain 1  score: 430.1 bits;  conditional E-value: 2e-133
                             TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                            +kk+ai+GyGsqG+a+a nlrdsg+ +v ++lr+++as kkAe  Gfkvl  ++a++ ad++miL pDe q 
  NCBI__GCF_000013325.1:WP_083760869.1  31 TDKKIAILGYGSQGHAHAQNLRDSGVkDVAIALRPGSASAKKAEAAGFKVLANADAAAWADILMILAPDEHQA 103
                                           79************************67********************************************* PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           + y  +++ ++k g+al f+HG ni+f  i++++d+dv+++APKgpG++vR+ey++g Gvp liAv+q+vtg+
  NCBI__GCF_000013325.1:WP_083760869.1 104 AIYADDLHANMKPGAALAFAHGLNIHFGLIEARADIDVIMIAPKGPGHTVRSEYQRGGGVPCLIAVHQNVTGN 176
                                           ************************************************************************* PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           a+++AlayA ++Gg+r g++et F+eE+e+DLfGEq+vLcGg +ali+a+f+tLveaGy+pe+Ayfe++helk
  NCBI__GCF_000013325.1:WP_083760869.1 177 AHDVALAYASGVGGGRSGIIETNFREECETDLFGEQVVLCGGTTALIQAGFETLVEAGYAPEMAYFECLHELK 249
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           livdll+e+G+++mr ++sntA++g+++++ +i++ee+kkem+ +l +iq+G+f k+++l+++ag+p++++ar
  NCBI__GCF_000013325.1:WP_083760869.1 250 LIVDLLYEGGIANMRYSISNTAEYGDIKTGpRIITEETKKEMKRVLADIQEGRFVKDFVLDNRAGQPELKAAR 322
                                           ************************************************************************* PP

                             TIGR00465 292 kkekeqeiekvGkelralvka 312
                                              k ++ie++G +lra++++
  NCBI__GCF_000013325.1:WP_083760869.1 323 GLAKRHQIEETGAKLRAMMPW 343
                                           *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (355 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: 00:00:00.00
# Mc/sec: 31.38
//
[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