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

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.3305.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: 00:00:00.03
# Mc/sec: 7.62
//
[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:

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 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 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