Alignments for a candidate for ilvD in Marinobacter adhaerens HP15

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.12236.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.33
//
[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