GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Marinobacter adhaerens HP15

Align Dihydroxy-acid dehydratase, mitochondrial; DAD; EC 4.2.1.9 (characterized)
to candidate GFF3421 HP15_3363 dihydroxy-acid dehydratase

Query= SwissProt::P39522
         (585 letters)



>FitnessBrowser__Marino:GFF3421
          Length = 562

 Score =  607 bits (1564), Expect = e-178
 Identities = 304/563 (53%), Positives = 397/563 (70%), Gaps = 11/563 (1%)

Query: 22  KLNKYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNRC 81
           K  KYS  + +  G+ AS+AML A GF  EDFKKPQ+G+ S W +  PCNMH+  L    
Sbjct: 9   KRRKYSAPVVDGIGKSASRAMLRAVGFTDEDFKKPQIGIASTWSNLTPCNMHINQLAEES 68

Query: 82  SQSIEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAIP 141
           +   ++AG K++ FNTI +SDGI+ GT+GM+YSL SRE+IADS ET+   + +D  +AI 
Sbjct: 69  AAGADEAGGKSLIFNTITISDGIANGTEGMKYSLVSREVIADSIETVAGCEGFDGLVAIG 128

Query: 142 SCDKNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISKQ 201
            CDKNMPG MM + R NRPS+ VYGGTI+PG           + DI+S F++ G +    
Sbjct: 129 GCDKNMPGCMMGLARLNRPSVFVYGGTIMPGE---------NHTDIISVFEAVGAHARGD 179

Query: 202 FTEEEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDNI 261
               E + + E A PGPGSCGGMYTANTMASA E +G+++P SS+  AVS+ K  +C   
Sbjct: 180 LDLIEVKQIEETAIPGPGSCGGMYTANTMASAIEAMGMSLPGSSAQNAVSETKAEDCRGA 239

Query: 262 GEYIKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDFQ 321
           G  +   +E  I P DI+T++AFENAIT V+A GGSTNAVLHL+A+A + GV L  +DF 
Sbjct: 240 GAAVLNLLEKDIKPSDIMTRKAFENAITVVIALGGSTNAVLHLLAMASTVGVDLELEDFV 299

Query: 322 RISDTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAKK 381
            I    P++ D +PSG Y+M++L+ +GG Q ++K L +  +LHG+ +TVTG TLAE    
Sbjct: 300 EIGKRVPVLADLRPSGHYMMSELVAIGGIQPLMKMLLDRGLLHGDCLTVTGQTLAENLAD 359

Query: 382 APSLPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEGA 441
               PEGQ+II    +PIKA+ HL+IL+G+LAP GAV KITGKEGT+F GRARVF  E  
Sbjct: 360 VDPYPEGQDIIHAFDNPIKADSHLRILFGNLAPTGAVAKITGKEGTHFTGRARVFHSEEE 419

Query: 442 FIEALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFSG 501
             E +  G +  G+  V+VIRYEGP+G PGM EML P+SA+MG GLG DVAL+TDGRFSG
Sbjct: 420 AQERILDGTVVAGD--VLVIRYEGPKGGPGMREMLSPTSAIMGKGLGSDVALITDGRFSG 477

Query: 502 GSHGFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPPR 561
           GSHGF++GHI PEAAEGGPI LV DGD I IDA +N+I+L VSD+E+ +R+Q+W APPPR
Sbjct: 478 GSHGFVVGHITPEAAEGGPIALVEDGDTITIDAVSNRIELDVSDQELERRRQAWQAPPPR 537

Query: 562 YTRGTLSKYAKLVSNASNGCVLD 584
           +TRGTL+KY++ VS+AS G V D
Sbjct: 538 FTRGTLAKYSRTVSSASKGAVTD 560


Lambda     K      H
   0.315    0.134    0.390 

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: 960
Number of extensions: 33
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: 585
Length of database: 562
Length adjustment: 36
Effective length of query: 549
Effective length of database: 526
Effective search space:   288774
Effective search space used:   288774
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate GFF3421 HP15_3363 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# 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/TIGR00110.hmm
# target sequence database:        /tmp/gapView.5152.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-231  755.4   5.9   1.9e-231  755.2   5.9    1.0  1  lcl|FitnessBrowser__Marino:GFF3421  HP15_3363 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3421  HP15_3363 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  755.2   5.9  1.9e-231  1.9e-231       1     542 [.      25     560 ..      25     561 .. 0.99

  Alignments for each domain:
  == domain 1  score: 755.2 bits;  conditional E-value: 1.9e-231
                           TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmk 75 
                                         a+ra+l+a+G++ded++kP+i++++++++++P+++h+++la+  +++ ++aGg++  fnti++sDGia g+eGmk
  lcl|FitnessBrowser__Marino:GFF3421  25 ASRAMLRAVGFTDEDFKKPQIGIASTWSNLTPCNMHINQLAEESAAGADEAGGKSLIFNTITISDGIANGTEGMK 99 
                                         589************************************************************************ PP

                           TIGR00110  76 ysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfe 150
                                         ysL+sre+iaDs+etv+  + +D+lv+i+ CDk++PG +m+ +rln+P+++v+GG++++g+ +     d+++vfe
  lcl|FitnessBrowser__Marino:GFF3421 100 YSLVSREVIADSIETVAGCEGFDGLVAIGGCDKNMPGCMMGLARLNRPSVFVYGGTIMPGENH----TDIISVFE 170
                                         ************************************************************998....699***** PP

                           TIGR00110 151 avgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrive 225
                                         avg+ a g+l+  e+++ie++a P++gsC+G++tan+ma++ ea+G+slPgss+ +a+s+ k+e ++ +g+ + +
  lcl|FitnessBrowser__Marino:GFF3421 171 AVGAHARGDLDLIEVKQIEETAIPGPGSCGGMYTANTMASAIEAMGMSLPGSSAQNAVSETKAEDCRGAGAAVLN 245
                                         *************************************************************************** PP

                           TIGR00110 226 lvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkvie 300
                                         l++k+ikP+di+t++afenait+++alGGstn+vLhlla+a+++gv+l+l+df ++ ++vP+la+l+Psg++++ 
  lcl|FitnessBrowser__Marino:GFF3421 246 LLEKDIKPSDIMTRKAFENAITVVIALGGSTNAVLHLLAMASTVGVDLELEDFVEIGKRVPVLADLRPSGHYMMS 320
                                         *************************************************************************** PP

                           TIGR00110 301 dlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGa 375
                                         +l + GG++ ++k+l  +gllh d+ltvtG+tlae+l++v+  +++qd+i++ dnp+k++++l++L+Gnla+ Ga
  lcl|FitnessBrowser__Marino:GFF3421 321 ELVAIGGIQPLMKMLLDRGLLHGDCLTVTGQTLAENLADVDPYPEGQDIIHAFDNPIKADSHLRILFGNLAPTGA 395
                                         *************************************************************************** PP

                           TIGR00110 376 vvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkva 450
                                         v+ki+g+e   ++f+G+a+vf+seeea e il+g v +Gdv+viryeGPkGgPGmremL Ptsa++g GLg++va
  lcl|FitnessBrowser__Marino:GFF3421 396 VAKITGKEG--THFTGRARVFHSEEEAQERILDGTVVAGDVLVIRYEGPKGGPGMREMLSPTSAIMGKGLGSDVA 468
                                         *********..**************************************************************** PP

                           TIGR00110 451 LitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaL 525
                                         LitDGrfsGg++G+++Gh++PeaaegG+ialvedGD+i+iD+ +++++l+vs++el++rr++++++ +r ++g+L
  lcl|FitnessBrowser__Marino:GFF3421 469 LITDGRFSGGSHGFVVGHITPEAAEGGPIALVEDGDTITIDAVSNRIELDVSDQELERRRQAWQAPPPRFTRGTL 543
                                         *************************************************************************** PP

                           TIGR00110 526 akyaklvssadkGavld 542
                                         aky++ vssa+kGav+d
  lcl|FitnessBrowser__Marino:GFF3421 544 AKYSRTVSSASKGAVTD 560
                                         ***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (562 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: 8.22
//
[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