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.3517343.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: 22.53
//
[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