Alignments for a candidate for ilvD in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfovibrio vulgaris Hildenborough

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate 208900 DVU3373 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>MicrobesOnline__882:208900
          Length = 554

 Score =  594 bits (1531), Expect = e-174
 Identities = 301/552 (54%), Positives = 402/552 (72%), Gaps = 7/552 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+S  +  G+++APHRSLL   GLT ++  +P +G+ N+  ++VPGHIHL ++AEAVK G
Sbjct: 1   MRSKKMTHGLEKAPHRSLLHALGLTREELARPLVGVVNAANEVVPGHIHLDDIAEAVKAG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V AAGG   EF  +A+CDG+AMNH+GM++SL SRE++AD++E MA AH  D LV +P CD
Sbjct: 61  VRAAGGTPLEFPAIAVCDGLAMNHEGMRFSLPSRELIADSIEIMATAHPFDALVFIPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           K VPGMLMA  RLD+P+++V+GGPML G     + DLI V+EGVG V  G+M+E EL+EL
Sbjct: 121 KSVPGMLMAMLRLDVPSVMVSGGPMLAGATLAGRADLITVFEGVGRVQRGDMTEAELDEL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
              ACPG  SCAG+FTAN+M CL E +G++LPG  T  AV++ + ++A+ +G +++EM++
Sbjct: 181 VEGACPGCGSCAGMFTANSMNCLAETIGLALPGNGTTPAVTAARIRLAKHAGMKVMEMLE 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
            N++P  I++++A  NAV VD+ALG STNT LH+PA+ AE  GL++ LD+FD++SR  P+
Sbjct: 241 RNIRPRDIVTEKAVANAVAVDMALGCSTNTVLHLPAVFAEA-GLDLTLDIFDKVSRKTPN 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLE--DHINRECVTCTGRTVQENIE--NVKVGHR 356
           +  +SPAG H + DL  AGGIPAV+  L+    I+R  +T TGRTV EN++    KV   
Sbjct: 300 LCKLSPAGHHHIQDLHAAGGIPAVMAELDRIGLIDRSAMTVTGRTVGENLDALGAKVRDA 359

Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416
           DVIRP+D+P   +GG+AIL+G+LAP G+VVKQ AVA +MMV E  A+VF+SE+   EAI 
Sbjct: 360 DVIRPVDAPYSPQGGIAILKGSLAPGGAVVKQSAVAPEMMVREAVARVFDSEEAACEAIM 419

Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVG 475
           GGRI  GD IVIRYEGPKGGPGMREML PTSAIAGMGL   VALITDGRFSGGTRG  +G
Sbjct: 420 GGRIKAGDAIVIRYEGPKGGPGMREMLTPTSAIAGMGLGADVALITDGRFSGGTRGAAIG 479

Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKG-WLAR 534
           HVSPEA E GP+  V +GD IRIDIP+R L++ +   E+  R  + V   + +    L R
Sbjct: 480 HVSPEAAEGGPIGLVQEGDRIRIDIPARALDLLVDEDELARRRAAFVPVEKEITSPLLRR 539

Query: 535 YRKLAGSADTGA 546
           Y ++  SA TGA
Sbjct: 540 YARMVSSAATGA 551


Lambda     K      H
   0.319    0.136    0.397 

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: 1008
Number of extensions: 53
Number of successful extensions: 5
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: 549
Length of database: 554
Length adjustment: 36
Effective length of query: 513
Effective length of database: 518
Effective search space:   265734
Effective search space used:   265734
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate 208900 DVU3373 (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.14587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.5e-238  776.4   7.5   8.5e-238  776.2   7.5    1.0  1  lcl|MicrobesOnline__882:208900  DVU3373 dihydroxy-acid dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208900  DVU3373 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  776.2   7.5  8.5e-238  8.5e-238       1     539 [.      14     551 ..      14     554 .] 0.99

  Alignments for each domain:
  == domain 1  score: 776.2 bits;  conditional E-value: 8.5e-238
                       TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysLp 79 
                                     ++r+ll+a+Gl+ e+l +P+++vvn+ +e+vPgh+hl+d+a++vk++++aaGg++ ef  iav+DG+am+heGm++sLp
  lcl|MicrobesOnline__882:208900  14 PHRSLLHALGLTREELARPLVGVVNAANEVVPGHIHLDDIAEAVKAGVRAAGGTPLEFPAIAVCDGLAMNHEGMRFSLP 92 
                                     69***************************************************************************** PP

                       TIGR00110  80 sreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgeyaag 158
                                     sre+iaDs+e +++ah +Dalv i++CDk vPGmlma+lrl++P+++vsGGpm ag t  + + dl+ vfe+vg+++ g
  lcl|MicrobesOnline__882:208900  93 SRELIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRLDVPSVMVSGGPMLAGATL-AGRADLITVFEGVGRVQRG 170
                                     ********************************************************999.6789*************** PP

                       TIGR00110 159 klseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknikPrdil 237
                                     +++e+el+e+++ acP++gsC+G+ftansm+cl+e++Gl+lPg++t++a++a + +lak++g++++e++++ni+Prdi+
  lcl|MicrobesOnline__882:208900 171 DMTEAELDELVEGACPGCGSCAGMFTANSMNCLAETIGLALPGNGTTPAVTAARIRLAKHAGMKVMEMLERNIRPRDIV 249
                                     ******************************************************************************* PP

                       TIGR00110 238 tkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeld 316
                                     t++a+ na+++d+alG stntvLhl+a+ +eag++l+ld fd++srk+P l+kl+P+g++ i+dlh+aGG++av+ eld
  lcl|MicrobesOnline__882:208900 250 TEKAVANAVAVDMALGCSTNTVLHLPAVFAEAGLDLTLDIFDKVSRKTPNLCKLSPAGHHHIQDLHAAGGIPAVMAELD 328
                                     ******************************************************************************* PP

                       TIGR00110 317 kegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakv 395
                                     + gl+++ a+tvtG+t++e+l+    +  d dvir++d p++ +gg+a+LkG+la+ Gavvk+++v+ ++++ e  a+v
  lcl|MicrobesOnline__882:208900 329 RIGLIDRSAMTVTGRTVGENLDALGAKVRDADVIRPVDAPYSPQGGIAILKGSLAPGGAVVKQSAVAPEMMVREAVARV 407
                                     ******************************************************************************* PP

                       TIGR00110 396 feseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaa 474
                                     f+see+a eai+gg++k+Gd +viryeGPkGgPGmremL+Ptsa++g+GLg +vaLitDGrfsGgtrG +iGhvsPeaa
  lcl|MicrobesOnline__882:208900 408 FDSEEAACEAIMGGRIKAGDAIVIRYEGPKGGPGMREMLTPTSAIAGMGLGADVALITDGRFSGGTRGAAIGHVSPEAA 486
                                     ******************************************************************************* PP

                       TIGR00110 475 egGaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGa 539
                                     egG+i+lv++GD+i+iDi++r+ldl v+e+ela+rra+ ++ e++ ++ +L++ya++vssa +Ga
  lcl|MicrobesOnline__882:208900 487 EGGPIGLVQEGDRIRIDIPARALDLLVDEDELARRRAAFVPVEKEITSPLLRRYARMVSSAATGA 551
                                     *******************************************99*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (554 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: 8.47
//
[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