GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Thiohalospira halophila DSM 15071 HL 3

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_093427733.1 BM272_RS05395 ketol-acid reductoisomerase

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



>NCBI__GCF_900112605.1:WP_093427733.1
          Length = 338

 Score =  489 bits (1258), Expect = e-143
 Identities = 238/338 (70%), Positives = 282/338 (83%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60
           M +FYDKDADLSLI+ + V I+GYGSQGHAHA NLK+SGV+V VGLR   AS  KA  AG
Sbjct: 1   MNIFYDKDADLSLIQKRKVAILGYGSQGHAHANNLKESGVDVVVGLRPGSASAAKAEQAG 60

Query: 61  LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120
           L V+ + +AV GAD+VM+L PDE    +Y   +  N+++GAALAFAHGFN+HYG + PRA
Sbjct: 61  LTVQSLDDAVAGADLVMVLAPDEHQGALYAEHIEPNLRQGAALAFAHGFNIHYGQIEPRA 120

Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180
           DLDVIMIAPK PGH VR+TYTQGGGVP LIAV Q+ SG ARDIAL+YA+ANGGGRAG+I+
Sbjct: 121 DLDVIMIAPKGPGHLVRSTYTQGGGVPSLIAVEQDSSGQARDIALAYASANGGGRAGVIQ 180

Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240
           T+FREETETDLFGEQAVLCGGT  L+KAGFETLVEAGYAPEMAYFECLHELKLIVDL+YE
Sbjct: 181 TSFREETETDLFGEQAVLCGGTSALVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300
           GGIANM YSISN AEYG++  G RVV E TK++M++ LT+IQ GE+A+ ++ EN+A AP 
Sbjct: 241 GGIANMRYSISNTAEYGDFTRGSRVVDEYTKESMREILTEIQNGEFAREWIAENQANAPV 300

Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           L + RRL AEHQIE+VG +LR MMPWIA NK+VD+SKN
Sbjct: 301 LKANRRLGAEHQIEQVGERLRGMMPWIASNKIVDRSKN 338


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: 459
Number of extensions: 12
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: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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_093427733.1 BM272_RS05395 (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.882026.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-141  456.2   0.5   2.8e-141  456.0   0.5    1.0  1  NCBI__GCF_900112605.1:WP_093427733.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093427733.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.0   0.5  2.8e-141  2.8e-141       1     312 [.      14     326 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.0 bits;  conditional E-value: 2.8e-141
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                           ++++kvai+GyGsqG+a+a nl++sg++v+vglr+++as +kAe+ G+ v ++++a++ adl+m+L pDe q 
  NCBI__GCF_900112605.1:WP_093427733.1  14 IQKRKVAILGYGSQGHAHANNLKESGVDVVVGLRPGSASAAKAEQAGLTVQSLDDAVAGADLVMVLAPDEHQG 86 
                                           5789********************************************************************* PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           + y ++i+p+l++g+al f+HGfni++ qi++++d+dv+++APKgpG+lvR++y +g GvpsliAveqd++g+
  NCBI__GCF_900112605.1:WP_093427733.1  87 ALYAEHIEPNLRQGAALAFAHGFNIHYGQIEPRADLDVIMIAPKGPGHLVRSTYTQGGGVPSLIAVEQDSSGQ 159
                                           ************************************************************************* PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           a++iAlayA a Gg+ragv++t+F+eE+e+DLfGEqavLcGg +al+ka+f+tLveaGy+pe+Ayfe++helk
  NCBI__GCF_900112605.1:WP_093427733.1 160 ARDIALAYASANGGGRAGVIQTSFREETETDLFGEQAVLCGGTSALVKAGFETLVEAGYAPEMAYFECLHELK 232
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           livdl++e+G+++mr ++sntA++g+++++ ++++e +k++m++il eiqnGefa+ew+ e++a++p +++ r
  NCBI__GCF_900112605.1:WP_093427733.1 233 LIVDLMYEGGIANMRYSISNTAEYGDFTRGsRVVDEYTKESMREILTEIQNGEFAREWIAENQANAPVLKANR 305
                                           ******************************9****************************************** PP

                             TIGR00465 292 kkekeqeiekvGkelralvka 312
                                           +   e++ie+vG++lr ++++
  NCBI__GCF_900112605.1:WP_093427733.1 306 RLGAEHQIEQVGERLRGMMPW 326
                                           *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (338 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: 00:00:00.00
# Mc/sec: 16.28
//
[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:

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