GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Marivita geojedonensis DPG-138

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_085640439.1 MGEO_RS16685 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_002115805.1:WP_085640439.1
          Length = 520

 Score =  487 bits (1253), Expect = e-142
 Identities = 259/504 (51%), Positives = 347/504 (68%), Gaps = 6/504 (1%)

Query: 1   MTQTN--RVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFE 58
           MTQT+  RV+IFDTTLRDGEQSPGA MT +EK+ +A  L+ +GVDIIEAGF  AS GDF 
Sbjct: 1   MTQTDKDRVVIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFR 60

Query: 59  AVNAIAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPK 118
           AV+ IA+    + +C L+RA   DI +  EAV  A + RIHTFI TSP+H      +   
Sbjct: 61  AVSEIAQRSKDAVICGLARAQLPDIDRCWEAVRHAKQPRIHTFIGTSPLHRAIP-NLTQD 119

Query: 119 QVIEAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSI 178
           ++ E   + V  AR   D+V++S  DA R+E D+L  +    I++GATTINIPDTVGY+ 
Sbjct: 120 EMAERIEQTVTHARNLCDNVQWSPMDATRTEWDYLCRVVEIAIKSGATTINIPDTVGYTA 179

Query: 179 PYKTEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERA 238
           P ++ +  R LI   P    VV++ HCHNDLG+A AN+LAA+ GGARQ+ECT+NGLGERA
Sbjct: 180 PVESADLIRRLIETVPGADDVVFATHCHNDLGMATANALAAVAGGARQIECTINGLGERA 239

Query: 239 GNASVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHE 298
           GN ++EE+VMALKVR D+    TGIDT +I+  S+ V+T++G+PVQ NKAIVG NAF+HE
Sbjct: 240 GNTALEEVVMALKVRGDIMPYTTGIDTKKIMHISRRVATVSGFPVQFNKAIVGKNAFAHE 299

Query: 299 SGIHQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNA 358
           SGIHQDG+LK+ ET+EIM  E VG A   L LGK SGR A + KL +LG+E+  +  L  
Sbjct: 300 SGIHQDGMLKNAETFEIMRPEDVGIAGTSLPLGKHSGRAALRAKLKELGVEV-GDNQLKD 358

Query: 359 AFARFKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIK 418
            F RFK+LAD+K+E+FD+D+ ALV+    +   ++ + ++ K+   TG    A +   I 
Sbjct: 359 IFVRFKDLADRKKEVFDDDILALVT--ATTEGDDALQLVNLKVVCGTGGPAEATLEMEIN 416

Query: 419 GEEKRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVV 478
           GE+K A + G GPVDA FKAI  +  + A LQ+Y V+AVT+GT++Q   SVRL     + 
Sbjct: 417 GEDKSAVSEGDGPVDATFKAIRMLHPNKARLQLYQVHAVTEGTDAQATVSVRLEEDGMIA 476

Query: 479 NGQGADTDVLVATAKAYLSALSKL 502
            GQ ADTD +VA+AKAY+ AL++L
Sbjct: 477 TGQSADTDTVVASAKAYIHALNRL 500


Lambda     K      H
   0.313    0.129    0.352 

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: 639
Number of extensions: 21
Number of successful extensions: 4
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: 517
Length of database: 520
Length adjustment: 35
Effective length of query: 482
Effective length of database: 485
Effective search space:   233770
Effective search space used:   233770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_085640439.1 MGEO_RS16685 (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.605078.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-202  658.9   2.1   2.3e-202  658.8   2.1    1.0  1  NCBI__GCF_002115805.1:WP_085640439.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085640439.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  658.8   2.1  2.3e-202  2.3e-202       1     494 []       8     498 ..       8     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 658.8 bits;  conditional E-value: 2.3e-202
                             TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglara 73 
                                           rv+ifdttlrdGeq+pga++t +ekl+ia+ l+++gvdiieaGfp++s+gdf av +ia++ k+a+++glara
  NCBI__GCF_002115805.1:WP_085640439.1   8 RVVIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFRAVSEIAQRSKDAVICGLARA 80 
                                           799********************************************************************** PP

                             TIGR00973  74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                              did  +ea++ a++ rihtfi ts++h++     t+de+ eri+++v++a+n+ d+v++s+ da+rte +
  NCBI__GCF_002115805.1:WP_085640439.1  81 QLPDIDRCWEAVRHAKQPRIHTFIGTSPLHRAIP-NLTQDEMAERIEQTVTHARNLCDNVQWSPMDATRTEWD 152
                                           ******************************9875.789*********************************** PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           +l+rvve ai++GattiniPdtvGy++P e ++li++l e+vP+ d+++++ hch+dlG+a+an+laav  Ga
  NCBI__GCF_002115805.1:WP_085640439.1 153 YLCRVVEIAIKSGATTINIPDTVGYTAPVESADLIRRLIETVPGADDVVFATHCHNDLGMATANALAAVAGGA 225
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafah 292
                                           rq+ectinG+GeraGn+aleevvmalkvr d+++++tgi+tk+i+++sr v+ ++g +vq nkaivG+nafah
  NCBI__GCF_002115805.1:WP_085640439.1 226 RQIECTINGLGERAGNTALEEVVMALKVRGDIMPYTTGIDTKKIMHISRRVATVSGFPVQFNKAIVGKNAFAH 298
                                           ************************************************************************* PP

                             TIGR00973 293 esGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkk 365
                                           esGihqdG+lkn et+ei++pe++G+  + l lgk+sGraal+ +l+elG+++ +++l+ +f +fk+lad+kk
  NCBI__GCF_002115805.1:WP_085640439.1 299 ESGIHQDGMLKNAETFEIMRPEDVGIAGTSLPLGKHSGRAALRAKLKELGVEVGDNQLKDIFVRFKDLADRKK 371
                                           ************************************************************************* PP

                             TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438
                                           evfd+d+ alv+  ++   ++ l+l++l+v +g+   + at++++++ge+k+a++ G Gpvda++kai  +  
  NCBI__GCF_002115805.1:WP_085640439.1 372 EVFDDDILALVTATTE--GDDALQLVNLKVVCGTGGPAEATLEMEINGEDKSAVSEGDGPVDATFKAIRMLHP 442
                                           ***********98776..45568************************************************** PP

                             TIGR00973 439 levklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                            + +l+ y+++a++eg+da++ v+v+le +g  ++G++++td v asakay++aln
  NCBI__GCF_002115805.1:WP_085640439.1 443 NKARLQLYQVHAVTEGTDAQATVSVRLEEDGMIATGQSADTDTVVASAKAYIHALN 498
                                           *******************************************************9 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 23.71
//
[ok]

This GapMind analysis is from Jul 26 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