Alignments for a candidate for leuA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Desulfovibrio vulgaris Hildenborough

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate 208494 DVU2981 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>MicrobesOnline__882:208494
          Length = 509

 Score =  529 bits (1363), Expect = e-155
 Identities = 273/498 (54%), Positives = 357/498 (71%), Gaps = 3/498 (0%)

Query: 6   RVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIAK 65
           R+ IFDTTLRDGEQSPGA M  +EK+R+A QL+ LGVDIIEAGF AASPGDFE+V AIAK
Sbjct: 4   RIRIFDTTLRDGEQSPGATMNIKEKLRLAHQLQTLGVDIIEAGFPAASPGDFESVRAIAK 63

Query: 66  TITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAAV 125
           T+   TV  L RA+  DI +A +AV  A   R+HTF+ATSP+HM+YKL+  P +V+    
Sbjct: 64  TVKGMTVAGLCRALPADIDRAWDAVCVAESPRLHTFLATSPVHMQYKLRKTPDEVVRMVD 123

Query: 126 KAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEEF 185
            AV+ A  +T +VEFS EDA RS+ DFL  +    IEAGATTINIPDTVGY+ P +    
Sbjct: 124 AAVRHAAGHTSNVEFSAEDASRSDRDFLVRVFTTAIEAGATTINIPDTVGYAQPEEFGAL 183

Query: 186 FRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVEE 245
            R +I  TPN  K V+S HCHNDLGL VAN+LAAL+ GARQ E T++G+GERAGNA++EE
Sbjct: 184 VRYVIENTPNAHKAVFSVHCHNDLGLGVANTLAALRAGARQAEVTISGIGERAGNAALEE 243

Query: 246 IVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQDG 305
           +VMAL+ RHD FGL+TGI T Q+ P+ +L+S I G P+  NKAIVGANAF+HESGIHQDG
Sbjct: 244 LVMALRTRHDYFGLDTGIVTEQLYPTCRLLSMIIGQPIPANKAIVGANAFAHESGIHQDG 303

Query: 306 VLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFKE 365
           +LKHRETYEIM+ ES+G     L LGK SGRNA K KL +LG  LE E+ LN  F   K+
Sbjct: 304 MLKHRETYEIMTPESIGRTRTELVLGKHSGRNAVKNKLEELGYRLE-EDQLNTVFDAVKQ 362

Query: 366 LADKKREIFDEDLHALVSDEMGSMNAESYKFISQKIS-TETGEEPRADIVFSIKGEEKRA 424
           LADKK++I DED+ ALV +E+  +  + Y+ ++  +  ++TG  P A +V  + GE  R 
Sbjct: 363 LADKKKQIHDEDVEALVLEEVYRI-PDRYRLVNLSVQCSDTGMPPTAAVVMEVDGETMRH 421

Query: 425 SATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGAD 484
           +  G+GP+DA+F AI  +      L+ YSV A+T GT++QGE +VR+        G+G+ 
Sbjct: 422 AGFGAGPIDAVFNAIAHIVGRTPQLERYSVTAITGGTDAQGEVTVRVRENGGTAVGRGSH 481

Query: 485 TDVLVATAKAYLSALSKL 502
            D+++A+A+AYL+AL++L
Sbjct: 482 PDIIIASARAYLNALNRL 499


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: 651
Number of extensions: 20
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: 509
Length adjustment: 35
Effective length of query: 482
Effective length of database: 474
Effective search space:   228468
Effective search space used:   228468
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 208494 DVU2981 (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.4933.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.1e-219  715.8   0.1   1.3e-219  715.7   0.1    1.0  1  lcl|MicrobesOnline__882:208494  DVU2981 2-isopropylmalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208494  DVU2981 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  715.7   0.1  1.3e-219  1.3e-219       1     494 []       4     497 ..       4     497 .. 0.99

  Alignments for each domain:
  == domain 1  score: 715.7 bits;  conditional E-value: 1.3e-219
                       TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdid 79 
                                     r+ ifdttlrdGeq+pga+++++ekl++a++l+ lgvdiieaGfp++s+gdfe+v+ ia++vk  +v+gl+ra+  did
  lcl|MicrobesOnline__882:208494   4 RIRIFDTTLRDGEQSPGATMNIKEKLRLAHQLQTLGVDIIEAGFPAASPGDFESVRAIAKTVKGMTVAGLCRALPADID 82 
                                     799**************************************************************************** PP

                       TIGR00973  80 aaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaaiea 158
                                      a++a+ +ae  r+htf+ats++h+++kl+kt dev+ ++ +av++a  ++ +vefsaeda+r++++fl+rv+ +aiea
  lcl|MicrobesOnline__882:208494  83 RAWDAVCVAESPRLHTFLATSPVHMQYKLRKTPDEVVRMVDAAVRHAAGHTSNVEFSAEDASRSDRDFLVRVFTTAIEA 161
                                     ******************************************************************************* PP

                       TIGR00973 159 GattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGeraGnaa 237
                                     GattiniPdtvGya P+e+g+l++++ en Pn +ka++svhch+dlGl van+laa+++Garq e+ti GiGeraGnaa
  lcl|MicrobesOnline__882:208494 162 GATTINIPDTVGYAQPEEFGALVRYVIENTPNAHKAVFSVHCHNDLGLGVANTLAALRAGARQAEVTISGIGERAGNAA 240
                                     ******************************************************************************* PP

                       TIGR00973 238 leevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesi 316
                                     lee+vmal++r+d+++++tgi t+++y t rl+s + g ++++nkaivG+nafahesGihqdG+lk++etyei++pesi
  lcl|MicrobesOnline__882:208494 241 LEELVMALRTRHDYFGLDTGIVTEQLYPTCRLLSMIIGQPIPANKAIVGANAFAHESGIHQDGMLKHRETYEIMTPESI 319
                                     ******************************************************************************* PP

                       TIGR00973 317 GlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqv 395
                                     G+++++lvlgk+sGr+a+k++leelG++l+e++l+ +f++ k+ladkkk+++ded+ealvlee+ + + ++++l++l+v
  lcl|MicrobesOnline__882:208494 320 GRTRTELVLGKHSGRNAVKNKLEELGYRLEEDQLNTVFDAVKQLADKKKQIHDEDVEALVLEEVYRIP-DRYRLVNLSV 397
                                     ****************************************************************9655.56******** PP

                       TIGR00973 396 qsgee.svptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkys 473
                                     q++++ + pta+v ++v+ge  + a  G+Gp+dav++ai +i++  ++l+ ys+ta + g+da+gev+v+++ ng ++ 
  lcl|MicrobesOnline__882:208494 398 QCSDTgMPPTAAVVMEVDGETMRHAGFGAGPIDAVFNAIAHIVGRTPQLERYSVTAITGGTDAQGEVTVRVRENGGTAV 476
                                     **9873678********************************************************************** PP

                       TIGR00973 474 Grgvatdiveasakayvnaln 494
                                     Grg + di+ asa+ay+naln
  lcl|MicrobesOnline__882:208494 477 GRGSHPDIIIASARAYLNALN 497
                                     ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (509 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.16
//
[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