Alignments for a candidate for ilvD in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Halomonas desiderata SP1

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_086508318.1 BZY95_RS01905 dihydroxy-acid dehydratase

Query= BRENDA::A0A481UJA7
         (614 letters)



>NCBI__GCF_002151265.1:WP_086508318.1
          Length = 561

 Score =  583 bits (1504), Expect = e-171
 Identities = 300/553 (54%), Positives = 388/553 (70%), Gaps = 4/553 (0%)

Query: 61  KYSSRITEPKSQGGSQAILHGVGLSDEDLNKPQIGISSVWYEGNTCNMHLLRLSEAVKEG 120
           ++S+ + +   +  S+A+L  VG SDED  KPQ+GI+S W     CN H+  L+E  ++G
Sbjct: 10  RHSAPVVDGVGKSASRAMLRAVGFSDEDFTKPQVGIASTWSMVTPCNSHIHELAERARDG 69

Query: 121 VKEAGMVGFRFNTIGVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPGCD 180
              AG  G  FNT+ +SD I+ GT GM YSL SR++IADSIETV   + +DG ++I GCD
Sbjct: 70  ADAAGGKGVIFNTVTISDGIANGTEGMKYSLVSREVIADSIETVAGCEGFDGLVAIGGCD 129

Query: 181 KNMPGTIMAMGRLNRPSIMVYGGTIKPGHYNGHSYDIISAFQAYGEYVNGSISDEDRKNV 240
           KNMPG +M + RLNRPS+ VYGGTI+PG    H+ DI+S F+A G +  G +   + K +
Sbjct: 130 KNMPGCLMGLARLNRPSVFVYGGTIQPG--KNHT-DIVSVFEAMGAHSRGDLELIELKQI 186

Query: 241 VHNSCPGAGACGGMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLELLK 300
              + PG G+CGGMYTANTMASAIEA+GM LP SS+  A +  K D+C  AG  +LELL+
Sbjct: 187 EETAIPGPGSCGGMYTANTMASAIEALGMSLPGSSAQNAVSQAKRDDCEAAGAAVLELLE 246

Query: 301 MDLKPQNIITPQSLRNAMVVVMALGGSTNAVLHLIPIARSVGLELTLEDFQKVSDEVPFL 360
            D+KP +I+T Q+  NA+ VV+ALGGSTNAVLHLI +A +VG+ L+L DF ++   VP L
Sbjct: 247 RDIKPSDIMTRQAFENAVTVVIALGGSTNAVLHLIAMANTVGVPLSLVDFTEIGRRVPVL 306

Query: 361 ADLKPSGKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEGQD 420
           ADL+PSG+Y+M ++ +IGG   +++ LL+ G L GDCLTVTG+TLAEN+ N  P  + Q 
Sbjct: 307 ADLRPSGRYMMSELVEIGGIQPLMKTLLDAGLLHGDCLTVTGRTLAENLANVAPYPDDQK 366

Query: 421 IIRPLENPIKKTGHIQILQGNLAPEGSVAKITGKEGLYFSGPALVFEGEEAMLAAISENP 480
           II  L+ P+K   H++IL GNLAPEG+VAKITGKEG  FSG A VF  EE   A I++  
Sbjct: 367 IIAALDAPLKAESHLRILFGNLAPEGAVAKITGKEGTRFSGTARVFGSEEEAQARINDGT 426

Query: 481 MNFKGKVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKDCALLTDGRFSGGSHGFVVGHI 540
           +   G VVVIR EGP+GGPGM EMLTPTSAIMG GLG   AL+TDGRFSGGSHGFVVGH+
Sbjct: 427 V-VAGDVVVIRYEGPRGGPGMREMLTPTSAIMGRGLGDSVALITDGRFSGGSHGFVVGHV 485

Query: 541 CPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQEMEERRKNWTPPPYKATCGVLYKYI 600
            PEA +GGP+ LV +GD+I ID     IDVD++D+E+  RR  W  P  + T GVL KY 
Sbjct: 486 TPEAFDGGPLALVEDGDMITIDAEADTIDVDLSDEELMRRRAAWQQPAPRYTRGVLAKYA 545

Query: 601 KNVQSASRGCVTD 613
           + V SAS G VTD
Sbjct: 546 RTVSSASTGAVTD 558


Lambda     K      H
   0.316    0.135    0.401 

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: 966
Number of extensions: 38
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: 614
Length of database: 561
Length adjustment: 37
Effective length of query: 577
Effective length of database: 524
Effective search space:   302348
Effective search space used:   302348
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 WP_086508318.1 BZY95_RS01905 (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.16145.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-227  742.6   5.3   1.4e-227  742.5   5.3    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508318.1  BZY95_RS01905 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508318.1  BZY95_RS01905 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  742.5   5.3  1.4e-227  1.4e-227       1     542 [.      23     558 ..      23     559 .. 0.99

  Alignments for each domain:
  == domain 1  score: 742.5 bits;  conditional E-value: 1.4e-227
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               a+ra+l+a+G++ded++kP+++++++++ ++P++ h+++la++++++ +aaGg+ + fnt+++sDGia 
  lcl|NCBI__GCF_002151265.1:WP_086508318.1  23 ASRAMLRAVGFSDEDFTKPQVGIASTWSMVTPCNSHIHELAERARDGADAAGGKGVIFNTVTISDGIAN 91 
                                               589****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+eGmkysL+sre+iaDs+etv+  + +D+lv+i+ CDk++PG lm+ +rln+P+++v+GG++++gk +
  lcl|NCBI__GCF_002151265.1:WP_086508318.1  92 GTEGMKYSLVSREVIADSIETVAGCEGFDGLVAIGGCDKNMPGCLMGLARLNRPSVFVYGGTIQPGKNH 160
                                               *******************************************************************99 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                    d+v+vfea+g+ + g+l+  el++ie++a P++gsC+G++tan+ma++ ealG+slPgss+ +a
  lcl|NCBI__GCF_002151265.1:WP_086508318.1 161 ----TDIVSVFEAMGAHSRGDLELIELKQIEETAIPGPGSCGGMYTANTMASAIEALGMSLPGSSAQNA 225
                                               ....699************************************************************** PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               +s+ k++ ++ +g+ + el++++ikP+di+t++afena+t+++alGGstn+vLhl+a+a+++gv lsl 
  lcl|NCBI__GCF_002151265.1:WP_086508318.1 226 VSQAKRDDCEAAGAAVLELLERDIKPSDIMTRQAFENAVTVVIALGGSTNAVLHLIAMANTVGVPLSLV 294
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               df ++ r+vP+la+l+Psg++++ +l + GG++ ++k+l  +gllh d+ltvtG+tlae+l++v   + 
  lcl|NCBI__GCF_002151265.1:WP_086508318.1 295 DFTEIGRRVPVLADLRPSGRYMMSELVEIGGIQPLMKTLLDAGLLHGDCLTVTGRTLAENLANVAPYPD 363
                                               ********************************************************************* PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               dq++i++ld p+k+e++l++L+Gnla+eGav+ki+g+e   ++f G+a+vf seeea + i +g v +G
  lcl|NCBI__GCF_002151265.1:WP_086508318.1 364 DQKIIAALDAPLKAESHLRILFGNLAPEGAVAKITGKEG--TRFSGTARVFGSEEEAQARINDGTVVAG 430
                                               ***************************************..**************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dvvviryeGP+GgPGmremL+Ptsa++g GLg++vaLitDGrfsGg++G+++Ghv+Pea  gG++alve
  lcl|NCBI__GCF_002151265.1:WP_086508318.1 431 DVVVIRYEGPRGGPGMREMLTPTSAIMGRGLGDSVALITDGRFSGGSHGFVVGHVTPEAFDGGPLALVE 499
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               dGD+i+iD+e+ ++d+++s+eel +rra+++++ +r+++g+Lakya+ vssa++Gav+d
  lcl|NCBI__GCF_002151265.1:WP_086508318.1 500 DGDMITIDAEADTIDVDLSDEELMRRRAAWQQPAPRYTRGVLAKYARTVSSASTGAVTD 558
                                               *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (561 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: 00:00:00.04
# Mc/sec: 7.57
//
[ok]

This GapMind analysis is from Apr 10 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