GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Dinoroseobacter shibae DFL-12

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate 3607175 Dshi_0596 2-isopropylmalate synthase (RefSeq)

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__Dino:3607175
          Length = 525

 Score =  482 bits (1240), Expect = e-140
 Identities = 256/503 (50%), Positives = 346/503 (68%), Gaps = 6/503 (1%)

Query: 2   TQTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVN 61
           T  +RV+IFDTTLRDGEQSPGA MT +EK+ +A  L+++GVDIIEAGF  AS GDF AV+
Sbjct: 5   TDQDRVLIFDTTLRDGEQSPGATMTHDEKLEIAALLDEMGVDIIEAGFPIASDGDFAAVS 64

Query: 62  AIAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVI 121
            IAK    S +C L+RA  +DI +  EAV  A + RIHTFI TSP+H      +   ++ 
Sbjct: 65  EIAKNSVNSVICGLARANFKDIDRCWEAVRHARQPRIHTFIGTSPLHRAIP-NLTMDEMA 123

Query: 122 EAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYK 181
           +     V  AR   D+V++S  DA R+E D+L  +    I+AGATTINIPDTVGY+ P +
Sbjct: 124 DRIHDTVTHARNLCDNVQWSPMDATRTEYDYLCRVIEIAIKAGATTINIPDTVGYTAPRE 183

Query: 182 TEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNA 241
           + +    LIA  P    V ++ HCHNDLG+A AN+LAA+  GARQVECT+NGLGERAGN 
Sbjct: 184 SADLIARLIADVPGAEDVTFATHCHNDLGMATANALAAVDAGARQVECTINGLGERAGNT 243

Query: 242 SVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGI 301
           ++EE+VMAL+VR+D+   +T IDT +I+  S+ V+ ++G+ VQ NKAIVG NAF+HESGI
Sbjct: 244 ALEEVVMALRVRNDIMPYQTRIDTRKIMNISRRVAAVSGFAVQFNKAIVGKNAFAHESGI 303

Query: 302 HQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFA 361
           HQDG+LK+ ET+EIM  E +G +   L +GK SGR A + KL DLG EL ++  L   F 
Sbjct: 304 HQDGMLKNAETFEIMRPEDIGLSETNLVMGKHSGRAALRAKLKDLGYEL-ADNQLKDVFV 362

Query: 362 RFKELADKKREIFDEDLHALVSDEMGSMNAE--SYKFISQKISTETGEEPRADIVFSIKG 419
           RFK LAD+K+EI+DEDL AL+S+       E  S KF+     TE  +   AD+  SI G
Sbjct: 363 RFKALADRKKEIYDEDLVALMSESSSDPARERLSVKFLRVICGTEAPQS--ADLTLSIDG 420

Query: 420 EEKRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVN 479
            +K+ +A G GPVDA F A++++    A LQ+Y V+AVT+GT++Q   +VR+    R+V+
Sbjct: 421 VDKQVTAQGDGPVDATFNAVKALFPHTARLQLYQVHAVTEGTDAQATVTVRMEEDGRIVS 480

Query: 480 GQGADTDVLVATAKAYLSALSKL 502
           GQ ADTD +VA+AKAY++AL++L
Sbjct: 481 GQAADTDTVVASAKAYVAALNRL 503


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: 617
Number of extensions: 14
Number of successful extensions: 3
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: 525
Length adjustment: 35
Effective length of query: 482
Effective length of database: 490
Effective search space:   236180
Effective search space used:   236180
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 3607175 Dshi_0596 (2-isopropylmalate synthase (RefSeq))
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.7609.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.2e-202  659.7   4.5   1.3e-202  659.5   4.5    1.0  1  lcl|FitnessBrowser__Dino:3607175  Dshi_0596 2-isopropylmalate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607175  Dshi_0596 2-isopropylmalate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  659.5   4.5  1.3e-202  1.3e-202       1     494 []       9     501 ..       9     501 .. 0.99

  Alignments for each domain:
  == domain 1  score: 659.5 bits;  conditional E-value: 1.3e-202
                         TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekd 77 
                                       rvlifdttlrdGeq+pga++t +ekl+ia  l+++gvdiieaGfp++s gdf av +ia++  n++++glara  kd
  lcl|FitnessBrowser__Dino:3607175   9 RVLIFDTTLRDGEQSPGATMTHDEKLEIAALLDEMGVDIIEAGFPIASDGDFAAVSEIAKNSVNSVICGLARANFKD 85 
                                       799************************************************************************** PP

                         TIGR00973  78 idaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvvea 154
                                       id  +ea++ a + rihtfi ts++h++     t+de+ +ri+ +v++a+n+ d+v++s+ da+rte ++l+rv+e 
  lcl|FitnessBrowser__Dino:3607175  86 IDRCWEAVRHARQPRIHTFIGTSPLHRAIP-NLTMDEMADRIHDTVTHARNLCDNVQWSPMDATRTEYDYLCRVIEI 161
                                       **************************9875.7899****************************************** PP

                         TIGR00973 155 aieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGe 231
                                       ai+aGattiniPdtvGy++P e ++li++l   vP+ ++++++ hch+dlG+a+an+laav++GarqvectinG+Ge
  lcl|FitnessBrowser__Dino:3607175 162 AIKAGATTINIPDTVGYTAPRESADLIARLIADVPGAEDVTFATHCHNDLGMATANALAAVDAGARQVECTINGLGE 238
                                       ***************************************************************************** PP

                         TIGR00973 232 raGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknkety 308
                                       raGn+aleevvmal+vr+d+++++t i+t++i+++sr v+ ++g +vq nkaivG+nafahesGihqdG+lkn et+
  lcl|FitnessBrowser__Dino:3607175 239 RAGNTALEEVVMALRVRNDIMPYQTRIDTRKIMNISRRVAAVSGFAVQFNKAIVGKNAFAHESGIHQDGMLKNAETF 315
                                       ***************************************************************************** PP

                         TIGR00973 309 eilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeee 385
                                       ei++pe+iGl++++lv+gk+sGraal+ +l++lG++l +++l+ +f +fk lad+kke++dedl+al++e+  ++ +
  lcl|FitnessBrowser__Dino:3607175 316 EIMRPEDIGLSETNLVMGKHSGRAALRAKLKDLGYELADNQLKDVFVRFKALADRKKEIYDEDLVALMSESSSDPAR 392
                                       ***************************************************************************** PP

                         TIGR00973 386 eklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevk 462
                                       e+l ++ l+v +g+e    a ++l ++g +k+ +a+G Gpvda+++a++ +     +l+ y+++a++eg+da++ v+
  lcl|FitnessBrowser__Dino:3607175 393 ERLSVKFLRVICGTEAPQSADLTLSIDGVDKQVTAQGDGPVDATFNAVKALFPHTARLQLYQVHAVTEGTDAQATVT 469
                                       ***************************************************************************** PP

                         TIGR00973 463 vvlelngkkysGrgvatdiveasakayvnaln 494
                                       v++e +g+ +sG++++td v asakayv aln
  lcl|FitnessBrowser__Dino:3607175 470 VRMEEDGRIVSGQAADTDTVVASAKAYVAALN 501
                                       ******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (525 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.86
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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