GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Sphingomonas indica Dd16

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_085219223.1 B9N75_RS13285 ketol-acid reductoisomerase

Query= SwissProt::Q9HVA2
         (338 letters)



>NCBI__GCF_900177405.1:WP_085219223.1
          Length = 327

 Score =  328 bits (841), Expect = 1e-94
 Identities = 166/322 (51%), Positives = 223/322 (69%), Gaps = 1/322 (0%)

Query: 1   MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGV-DVTVGLRSGSATVAKAEAH 59
           MR  +D D DL++I+ +KVAI GYG+QG   A NL DSGV ++ V LR GSA+ A+AEA 
Sbjct: 1   MRALFDADADLALIRDRKVAIFGYGNQGRPQALNLSDSGVGELVVALREGSASRARAEAD 60

Query: 60  GLKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPR 119
            L V ++  A A ADV ++L PDE Q  +Y+  + P+LK+GA L FAHG +I +  +VPR
Sbjct: 61  RLGVTNLADAAAWADVAVMLFPDEDQAEVYERHLAPHLKQGAALVFAHGLAIRFGLIVPR 120

Query: 120 ADLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGII 179
           ADLDV+++APK PG  +RSE+  G G+  L A+ QDASG A+ +ALSYA  +GGGR G+I
Sbjct: 121 ADLDVMLVAPKGPGTALRSEYAAGRGLVTLFAVAQDASGGAEALALSYAAALGGGRAGMI 180

Query: 180 ETTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMY 239
           ET+F +E E DLF E AV+ G   EL++AGF+TLVEAG++PE+AYFECL E+KLI DL+ 
Sbjct: 181 ETSFAEECEADLFNEAAVIWGAIPELIQAGFDTLVEAGFSPEVAYFECLTEVKLIADLIT 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYP 299
           E GIA M  +ISN AE+G    G  ++ AE+R  MR  L+ +++G  A+  I +  A YP
Sbjct: 241 ERGIAGMREAISNTAEFGALEGGRRIVTAETRTEMRRILRDVREGHLAQRLIADAKAGYP 300

Query: 300 SMTAYRRNNAAHPIEQIGEKLR 321
            + A R   AAHPIE  G +LR
Sbjct: 301 RLKASRAEAAAHPIEAAGARLR 322


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: 289
Number of extensions: 11
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: 327
Length adjustment: 28
Effective length of query: 310
Effective length of database: 299
Effective search space:    92690
Effective search space used:    92690
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_085219223.1 B9N75_RS13285 (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.3728286.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-109  349.3   0.0   9.6e-109  349.1   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085219223.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085219223.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.1   0.0  9.6e-109  9.6e-109       2     310 ..      15     325 ..      14     327 .] 0.99

  Alignments for each domain:
  == domain 1  score: 349.1 bits;  conditional E-value: 9.6e-109
                             TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                           +++kvai GyG qG+ qalnl dsg+ +++v+lr+++as ++Ae d + v+++++a++ ad+ ++L pDe q 
  NCBI__GCF_900177405.1:WP_085219223.1  15 RDRKVAIFGYGNQGRPQALNLSDSGVgELVVALREGSASRARAEADRLGVTNLADAAAWADVAVMLFPDEDQA 87 
                                           689***********************7799******************************************* PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           evye++++p lk+g+al+f+HG  i f  iv+++d+dv+lvAPKgpG+++R+ey  grG+ +l+Av qd++g 
  NCBI__GCF_900177405.1:WP_085219223.1  88 EVYERHLAPHLKQGAALVFAHGLAIRFGLIVPRADLDVMLVAPKGPGTALRSEYAAGRGLVTLFAVAQDASGG 160
                                           ************************************************************************* PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           a + Al+yA+a+Gg+rag++et+F eE+e+DLf E av+ G + +li+a+fdtLveaG +pe+Ayfe++ e+k
  NCBI__GCF_900177405.1:WP_085219223.1 161 AEALALSYAAALGGGRAGMIETSFAEECEADLFNEAAVIWGAIPELIQAGFDTLVEAGFSPEVAYFECLTEVK 233
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           li+dl++e+G+++mr+a+sntA++gale + +i+++e+++em+ il ++++G+ a+  + + +ag+p++++ r
  NCBI__GCF_900177405.1:WP_085219223.1 234 LIADLITERGIAGMREAISNTAEFGALEGGrRIVTAETRTEMRRILRDVREGHLAQRLIADAKAGYPRLKASR 306
                                           ****************************9999***************************************** PP

                             TIGR00465 292 kkekeqeiekvGkelralv 310
                                                + ie  G +lr+l 
  NCBI__GCF_900177405.1:WP_085219223.1 307 AEAAAHPIEAAGARLRNLA 325
                                           ****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (327 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: 25.79
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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