GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Thermus aquaticus YT-1

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_053768623.1 BVI061214_RS07985 2-isopropylmalate synthase

Query= BRENDA::Q72JC9
         (520 letters)



>NCBI__GCF_001280255.1:WP_053768623.1
          Length = 520

 Score =  950 bits (2455), Expect = 0.0
 Identities = 478/520 (91%), Positives = 507/520 (97%)

Query: 1   MEKERHIRIFDTTLRDGEQSPGVALSLDQKLEIAQALAQLNVDIIEAGFPVSGPMEFEAV 60
           MEKERHIRIFDTTLRDGEQSPGVALSLDQKLEIA ALA+LNVDIIEAGFPVSGP+EFEAV
Sbjct: 1   MEKERHIRIFDTTLRDGEQSPGVALSLDQKLEIAHALARLNVDIIEAGFPVSGPLEFEAV 60

Query: 61  RRIATEVKGPIIAALARTHTLDIDQAAKALEKAEKPRIHVFTSASKVHLQYMLRKTEEEV 120
           RRIA EVKGP+IAALARTHTLDIDQAA+ALEKAEKPRIHVFTSASK+HLQYML+KTEEEV
Sbjct: 61  RRIAAEVKGPVIAALARTHTLDIDQAARALEKAEKPRIHVFTSASKIHLQYMLKKTEEEV 120

Query: 121 LEMADRMVRYARRYVDDVEFSAQDVMRADWEFVKRLYEVAIEAGATTINIPDTTGYGTPQ 180
           LEMAD MVRYAR+YVDDVEFSAQDVMRA+W+FVKRLYEVAIEAGATT+NIPDTTGYGTP+
Sbjct: 121 LEMADEMVRYARKYVDDVEFSAQDVMRAEWDFVKRLYEVAIEAGATTVNIPDTTGYGTPE 180

Query: 181 EYGALIRRIRDEVVRGRDVIISTHTHDDLGMATANALAGVENGAGQIECTINGIGERAGN 240
           EYGALIRRIRDEVVRGRDV+ISTHTHDDLG+ATANALAGV NGAGQ+ECT+NGIGERAGN
Sbjct: 181 EYGALIRRIRDEVVRGRDVVISTHTHDDLGLATANALAGVLNGAGQVECTVNGIGERAGN 240

Query: 241 CALEEVVMALYVRRDWYKAYTRINTREIYRVSRLVERYTGMPVPPNKAIVGDNAFAHESG 300
            ALEEVVMALYVRRD+YKAYT+INTREIYRVSRLVERYTGMPVPPNKAIVGDNAFAHESG
Sbjct: 241 TALEEVVMALYVRRDFYKAYTQINTREIYRVSRLVERYTGMPVPPNKAIVGDNAFAHESG 300

Query: 301 IHQDGVIKHRATYEIMDAELIGRRPAVLVLGKHSGRAAFKKALEDLGYKDLSEEEVKKLF 360
           IHQDGV+KHR TYEIMDAELIGRRPAVLVLGKHSGRAAF+KALEDLGYKDL+EE++K LF
Sbjct: 301 IHQDGVLKHRGTYEIMDAELIGRRPAVLVLGKHSGRAAFRKALEDLGYKDLTEEQLKVLF 360

Query: 361 ARFKEIAEKKGPLSAEELQALVESEREPTSHFFQLEHVQFFSGSGLLPTATVKVKTPDGE 420
           +RFKEIAEKKGPLSAEELQALVE+  EP S FF+L+HVQFFSGSGLLPTATV+V TPDGE
Sbjct: 361 SRFKEIAEKKGPLSAEELQALVETGLEPASRFFELKHVQFFSGSGLLPTATVRVMTPDGE 420

Query: 421 RVATHTGDGPVDAVYKAIQEAIGLRPELELYRVEAITGSTEALGQVTVRLRLGELQAVGV 480
           RVATHTGDGPVDAVYKAI+EAIGL+PELELYRVEAITGSTEALGQVTVRLRLGELQAVGV
Sbjct: 421 RVATHTGDGPVDAVYKAIEEAIGLKPELELYRVEAITGSTEALGQVTVRLRLGELQAVGV 480

Query: 481 GVSPDIIEASALAFLDAAGKLASGRATRHPPSIEEVHRGV 520
           GVSPDIIEASALAFLDAAGKLASGRATRHPPSIEEV RGV
Sbjct: 481 GVSPDIIEASALAFLDAAGKLASGRATRHPPSIEEVQRGV 520


Lambda     K      H
   0.318    0.134    0.378 

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: 1033
Number of extensions: 21
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: 520
Length of database: 520
Length adjustment: 35
Effective length of query: 485
Effective length of database: 485
Effective search space:   235225
Effective search space used:   235225
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: 52 (24.6 bits)

Align candidate WP_053768623.1 BVI061214_RS07985 (2-isopropylmalate synthase)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.1870530.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-206  673.1   0.1   1.2e-206  672.9   0.1    1.0  1  NCBI__GCF_001280255.1:WP_053768623.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053768623.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.9   0.1  1.2e-206  1.2e-206       2     492 ..       7     497 ..       6     499 .. 0.99

  Alignments for each domain:
  == domain 1  score: 672.9 bits;  conditional E-value: 1.2e-206
                             TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglarav 74 
                                           + ifdttlrdGeq+pg++l++++kl+ia+al+rl+vdiieaGfpvs + +feav++ia evk +++++lar+ 
  NCBI__GCF_001280255.1:WP_053768623.1   7 IRIFDTTLRDGEQSPGVALSLDQKLEIAHALARLNVDIIEAGFPVSGPLEFEAVRRIAAEVKGPVIAALARTH 79 
                                           89*********************************************************************** PP

                             TIGR00973  75 ekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtelef 147
                                             did aa+al++aek rih+f ++s+ihl++ lkkt++evle++ ++v+ya+++vddvefsa+d  r+e +f
  NCBI__GCF_001280255.1:WP_053768623.1  80 TLDIDQAARALEKAEKPRIHVFTSASKIHLQYMLKKTEEEVLEMADEMVRYARKYVDDVEFSAQDVMRAEWDF 152
                                           ************************************************************************* PP

                             TIGR00973 148 larvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGar 220
                                           + r++e aieaGatt+niPdt Gy +P+eyg+li++++++v    ++++s h+hddlGla+an+la v nGa 
  NCBI__GCF_001280255.1:WP_053768623.1 153 VKRLYEVAIEAGATTVNIPDTTGYGTPEEYGALIRRIRDEVVRGRDVVISTHTHDDLGLATANALAGVLNGAG 225
                                           ************************************************************************* PP

                             TIGR00973 221 qvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahe 293
                                           qvect+nGiGeraGn+aleevvmal vr+df++ +t+int+eiyr+srlv + tgm+v++nkaivGdnafahe
  NCBI__GCF_001280255.1:WP_053768623.1 226 QVECTVNGIGERAGNTALEEVVMALYVRRDFYKAYTQINTREIYRVSRLVERYTGMPVPPNKAIVGDNAFAHE 298
                                           ************************************************************************* PP

                             TIGR00973 294 sGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfk.ldeeeldklfekfkeladkkk 365
                                           sGihqdGvlk++ tyei+++e iG++   lvlgk+sGraa++k le+lG+k l+ee+l+ lf++fke+a+kk+
  NCBI__GCF_001280255.1:WP_053768623.1 299 SGIHQDGVLKHRGTYEIMDAELIGRRPAVLVLGKHSGRAAFRKALEDLGYKdLTEEQLKVLFSRFKEIAEKKG 371
                                           **************************************************747999***************** PP

                             TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438
                                            +  e+l+alv + l+ + ++ ++l+++q  sg+  +ptatv++ +++ e+ a++tG Gpvdavykaie++++
  NCBI__GCF_001280255.1:WP_053768623.1 372 PLSAEELQALVETGLE-PASRFFELKHVQFFSGSGLLPTATVRVMTPDGERVATHTGDGPVDAVYKAIEEAIG 443
                                           ************9998.77777*************************************************** PP

                             TIGR00973 439 levklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvna 492
                                           l+++l+ y+++a + +++alg+v+v+l+l + ++ G+gv+ di+easa a+++a
  NCBI__GCF_001280255.1:WP_053768623.1 444 LKPELELYRVEAITGSTEALGQVTVRLRLGELQAVGVGVSPDIIEASALAFLDA 497
                                           ****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (520 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: 30.39
//
[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