GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Novosphingobium barchaimii LL02

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_059150279.1 V474_RS04405 ketol-acid reductoisomerase

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



>NCBI__GCF_001046635.1:WP_059150279.1
          Length = 339

 Score =  456 bits (1172), Expect = e-133
 Identities = 218/339 (64%), Positives = 268/339 (79%), Gaps = 1/339 (0%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVN-VTVGLRKSGASWNKAANA 59
           MKV+YD D+D++LI  K + ++GYGSQGHAHA NL+DSGV  V + LR+  A+  KA  A
Sbjct: 1   MKVYYDADSDINLITDKKIVVLGYGSQGHAHAQNLRDSGVKEVAIALREGSATAKKAEGA 60

Query: 60  GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119
           G +V    +A   AD++MIL PDE  A +Y  ++H N+K GAALAFAHG NVH+G + PR
Sbjct: 61  GFKVMSNKDAAAWADIIMILAPDEHQAAIYAEDLHANMKPGAALAFAHGLNVHFGLIEPR 120

Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179
            D+DVIMIAPK PGHTVR+ Y +GGGVP L+A+HQ+ +G A D+AL+YA+  GGGR+GII
Sbjct: 121 TDIDVIMIAPKGPGHTVRSEYQRGGGVPCLVAIHQDVTGNAHDVALAYASGVGGGRSGII 180

Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239
           ETNFREE ETDLFGEQAVLCGG   L++AGFETLVEAGYAPEMAYFECLHELKLIVDL+Y
Sbjct: 181 ETNFREECETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECLHELKLIVDLMY 240

Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299
           EGGIANM YSISN AEYG+  TGPR++TEETKK MK+ L DIQ+G + K F+++N+AG P
Sbjct: 241 EGGIANMRYSISNTAEYGDIKTGPRIITEETKKEMKRVLEDIQSGRFVKDFVMDNRAGQP 300

Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
            L + R+    H IEE GAKLRAMMPWIA N +VD++KN
Sbjct: 301 ELKASRKAALRHPIEETGAKLRAMMPWIAANALVDKAKN 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: 449
Number of extensions: 20
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_059150279.1 V474_RS04405 (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.883955.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-134  433.1   0.6   3.1e-134  432.8   0.6    1.0  1  NCBI__GCF_001046635.1:WP_059150279.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059150279.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.8   0.6  3.1e-134  3.1e-134       2     312 ..      15     327 ..      14     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 432.8 bits;  conditional E-value: 3.1e-134
                             TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsgln.vivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                            +kk++++GyGsqG+a+a nlrdsg++ v ++lr+++a+ kkAe  Gfkv++ ++a++ ad+imiL pDe q 
  NCBI__GCF_001046635.1:WP_059150279.1  15 TDKKIVVLGYGSQGHAHAQNLRDSGVKeVAIALREGSATAKKAEGAGFKVMSNKDAAAWADIIMILAPDEHQA 87 
                                           79************************559******************************************** PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           + y ++++ ++k g+al f+HG n++f  i+++ d+dv+++APKgpG++vR+ey++g Gvp l+A++qdvtg+
  NCBI__GCF_001046635.1:WP_059150279.1  88 AIYAEDLHANMKPGAALAFAHGLNVHFGLIEPRTDIDVIMIAPKGPGHTVRSEYQRGGGVPCLVAIHQDVTGN 160
                                           ************************************************************************* PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           a+++AlayA ++Gg+r g++et F+eE+e+DLfGEqavLcGg +al++a+f+tLveaGy+pe+Ayfe++helk
  NCBI__GCF_001046635.1:WP_059150279.1 161 AHDVALAYASGVGGGRSGIIETNFREECETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECLHELK 233
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           livdl++e+G+++mr ++sntA++g+++++ +i++ee+kkem+ +l++iq+G+f k+++++++ag+p++++ r
  NCBI__GCF_001046635.1:WP_059150279.1 234 LIVDLMYEGGIANMRYSISNTAEYGDIKTGpRIITEETKKEMKRVLEDIQSGRFVKDFVMDNRAGQPELKASR 306
                                           ************************************************************************* PP

                             TIGR00465 292 kkekeqeiekvGkelralvka 312
                                           k+   + ie++G +lra++++
  NCBI__GCF_001046635.1:WP_059150279.1 307 KAALRHPIEETGAKLRAMMPW 327
                                           *******************97 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 18.11
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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