Alignments for a candidate for ilvC in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Sphingomonas wittichii RW1

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_011951459.1 SWIT_RS03110 ketol-acid reductoisomerase

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



>NCBI__GCF_000016765.1:WP_011951459.1
          Length = 339

 Score =  461 bits (1185), Expect = e-134
 Identities = 226/339 (66%), Positives = 274/339 (80%), Gaps = 1/339 (0%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59
           M+V+YD+DAD+ LIK K V I+GYGSQGHAHA NL+DSGV +V + LR   A+  KA  A
Sbjct: 1   MRVYYDRDADIGLIKTKKVAIVGYGSQGHAHAQNLQDSGVADVAIALRPGSATAKKAEGA 60

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           G +V   A+A K AD+VMIL PDE  A +Y +++ DN+K GAALAFAHG NVH+G + PR
Sbjct: 61  GFKVLSNADAAKWADIVMILAPDEHQAAIYNDDLRDNLKPGAALAFAHGLNVHFGLIEPR 120

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
           AD+DV MIAPK PGHTVR+ Y +GGGVP LIA+ Q+ SG A D+ALSYA+A GGGR+G+I
Sbjct: 121 ADIDVFMIAPKGPGHTVRSEYQRGGGVPCLIAIAQDASGNAHDVALSYASAIGGGRSGVI 180

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ET F+EE ETDLFGEQAVLCGG   LI AGFETLVEAGYAPEMAYFECLHE+KLIVDL+Y
Sbjct: 181 ETTFKEECETDLFGEQAVLCGGLSHLIMAGFETLVEAGYAPEMAYFECLHEVKLIVDLMY 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299
           EGGIANM YSISN AEYG+  TGPRV+T ETK  MK+ L DIQ G++ K F+L+N+AG P
Sbjct: 241 EGGIANMRYSISNTAEYGDIHTGPRVITSETKAEMKRVLDDIQKGKFVKRFVLDNRAGQP 300

Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
            L + R+L AEH IE+VGA+LRAMMPWI+KN++VD++KN
Sbjct: 301 ELKASRKLVAEHPIEKVGAELRAMMPWISKNQLVDKAKN 339


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: 413
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: 338
Length of database: 339
Length adjustment: 28
Effective length of query: 310
Effective length of database: 311
Effective search space:    96410
Effective search space used:    96410
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_011951459.1 SWIT_RS03110 (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.31831.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.8e-135  434.8   0.1   9.2e-135  434.6   0.1    1.0  1  lcl|NCBI__GCF_000016765.1:WP_011951459.1  SWIT_RS03110 ketol-acid reductoi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_011951459.1  SWIT_RS03110 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.6   0.1  9.2e-135  9.2e-135       1     312 [.      14     327 ..      14     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 434.6 bits;  conditional E-value: 9.2e-135
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlp 68 
                                               +k kkvai+GyGsqG+a+a nl+dsg+ +v ++lr+++a+ kkAe  Gfkvl+ ++a+k ad++miL p
  lcl|NCBI__GCF_000016765.1:WP_011951459.1  14 IKTKKVAIVGYGSQGHAHAQNLQDSGVaDVAIALRPGSATAKKAEGAGFKVLSNADAAKWADIVMILAP 82 
                                               589***********************978**************************************** PP

                                 TIGR00465  69 DevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsli 137
                                               De q + y+ +++++lk g+al f+HG n++f  i++++d+dv+++APKgpG++vR+ey++g Gvp li
  lcl|NCBI__GCF_000016765.1:WP_011951459.1  83 DEHQAAIYNDDLRDNLKPGAALAFAHGLNVHFGLIEPRADIDVFMIAPKGPGHTVRSEYQRGGGVPCLI 151
                                               ********************************************************************* PP

                                 TIGR00465 138 AveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyq 206
                                               A+ qd++g+a+++Al+yA aiGg+r gv+ettFkeE+e+DLfGEqavLcGgl+ li a+f+tLveaGy+
  lcl|NCBI__GCF_000016765.1:WP_011951459.1 152 AIAQDASGNAHDVALSYASAIGGGRSGVIETTFKEECETDLFGEQAVLCGGLSHLIMAGFETLVEAGYA 220
                                               ********************************************************************* PP

                                 TIGR00465 207 pelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefak 274
                                               pe+Ayfe++he+klivdl++e+G+++mr ++sntA++g+++++ ++++ e+k+em+ +l++iq+G+f k
  lcl|NCBI__GCF_000016765.1:WP_011951459.1 221 PEMAYFECLHEVKLIVDLMYEGGIANMRYSISNTAEYGDIHTGpRVITSETKAEMKRVLDDIQKGKFVK 289
                                               ********************************************************************* PP

                                 TIGR00465 275 ewalekeagkpafeearkkekeqeiekvGkelralvka 312
                                                ++l+++ag+p++++ rk   e+ iekvG elra++++
  lcl|NCBI__GCF_000016765.1:WP_011951459.1 290 RFVLDNRAGQPELKASRKLVAEHPIEKVGAELRAMMPW 327
                                               ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (339 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.29
//
[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