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.16977.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.64
//
[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