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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis