Alignments for a candidate for ilvD in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Hydrogenophaga taeniospiralis NBRC 102512

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_068175560.1 HTA01S_RS22645 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_001592305.1:WP_068175560.1
          Length = 615

 Score =  919 bits (2375), Expect = 0.0
 Identities = 458/613 (74%), Positives = 516/613 (84%), Gaps = 3/613 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRS+T+T GRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPAYRSKTSTAGRNMAGARSLWRATGMKDGDFDKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR++IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHA--LDLVDAMVAAADDKISD 178
           NCDKITPGMLMA++RLNIP VFVSGGPMEAGK  + G      LDL+DAMV AAD K+SD
Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKTRLAGSIEIKKLDLIDAMVMAADVKVSD 180

Query: 179 EDVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHL 238
            D+  +ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH DR++LF  AG L
Sbjct: 181 ADLAEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLFKRAGRL 240

Query: 239 IVDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTM 298
            VDL RRYYEQDD   LPR++  K AFENA+TLDIAMGGSTNT+LH+LA A E EIDFTM
Sbjct: 241 AVDLCRRYYEQDDASVLPRSMGFK-AFENAITLDIAMGGSTNTILHLLAIAQEAEIDFTM 299

Query: 299 ADIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLG 358
            DID LSR VP L KVAP  +  H+EDVHRAGGIM+ILGELD+ G L+ D PTVHA T+ 
Sbjct: 300 KDIDRLSRVVPQLCKVAPNTNKYHIEDVHRAGGIMAILGELDRAGKLHTDVPTVHARTMK 359

Query: 359 DAIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSK 418
           DA+D+WDI R  S  V+ FYRA P G+P+QVAFSQ  RW  LDTDR  G IRS EH FS+
Sbjct: 360 DALDQWDIARNPSAEVQTFYRAGPAGVPSQVAFSQSTRWPSLDTDRAEGCIRSGEHAFSQ 419

Query: 419 DGGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVI 478
           +GGLAVL GN+A++GC+VKTAGVD+++L F G A V ESQD +V  IL ++VKAGDVV++
Sbjct: 420 EGGLAVLVGNIALNGCVVKTAGVDDALLVFEGTAHVTESQDEAVANILDDKVKAGDVVIV 479

Query: 479 RYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTI 538
           RYEGPKGGPGMQEMLYPTSY+KSKGLGKACAL+TDGRFSGGTSGLSIGH SPEAA GG I
Sbjct: 480 RYEGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAI 539

Query: 539 GLVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFA 598
           GLVR GD I IDIPNR+I++ VS+ ELA RR+EQDAKGW P   RKR V+ ALKAYA  A
Sbjct: 540 GLVRNGDRIRIDIPNRSINVLVSDDELAQRRSEQDAKGWKPALPRKRKVSAALKAYALLA 599

Query: 599 TSADRGAVRDLNV 611
            SAD+GAVRDL++
Sbjct: 600 MSADKGAVRDLSL 612


Lambda     K      H
   0.318    0.134    0.391 

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: 1189
Number of extensions: 26
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: 612
Length of database: 615
Length adjustment: 37
Effective length of query: 575
Effective length of database: 578
Effective search space:   332350
Effective search space used:   332350
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_068175560.1 HTA01S_RS22645 (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.8701.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-256  835.8   3.0   8.7e-256  835.6   3.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068175560.1  HTA01S_RS22645 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068175560.1  HTA01S_RS22645 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  835.6   3.0  8.7e-256  8.7e-256       2     542 ..      18     609 ..      17     610 .. 0.98

  Alignments for each domain:
  == domain 1  score: 835.6 bits;  conditional E-value: 8.7e-256
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar+l++atG+kd d++kPiia++ns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamg
  lcl|NCBI__GCF_001592305.1:WP_068175560.1  18 ARSLWRATGMKDGDFDKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMG 86 
                                               69******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsr+iiaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+++vsGGpmeagkt+l
  lcl|NCBI__GCF_001592305.1:WP_068175560.1  87 HDGMLYSLPSRDIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKTRL 155
                                               *******************************************************************99 PP

                                 TIGR00110 140 ..sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206
                                                 s +i+++d+++a++++a+ k+s+++l e+ersacPt+gsCsG+ftansm+cltealGlslPg++t+ 
  lcl|NCBI__GCF_001592305.1:WP_068175560.1 156 agSIEIKKLDLIDAMVMAADVKVSDADLAEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVV 224
                                               657788999************************************************************ PP

                                 TIGR00110 207 atsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiake 268
                                               at+a++++l+k++g+  v+l++++++       Pr++   +afenaitld+a+GGstnt+Lhllaia+e
  lcl|NCBI__GCF_001592305.1:WP_068175560.1 225 ATHADREQLFKRAGRLAVDLCRRYYEqddasvlPRSM-GFKAFENAITLDIAMGGSTNTILHLLAIAQE 292
                                               **************************99999988885.689**************************** PP

                                 TIGR00110 269 agvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaet 336
                                               a+++++++d+drlsr vP+l+k++P+++k+ ied+hraGG++a+l+eld++g+lh+d+ tv  +t+++ 
  lcl|NCBI__GCF_001592305.1:WP_068175560.1 293 AEIDFTMKDIDRLSRVVPQLCKVAPNTNKYhIEDVHRAGGIMAILGELDRAGKLHTDVPTVHARTMKDA 361
                                               *****************************99************************************** PP

                                 TIGR00110 337 lekvkvlr...................................vdqd..virsldnpvkkegglavLkG 368
                                               l++ ++ r                                         +irs ++++++egglavL G
  lcl|NCBI__GCF_001592305.1:WP_068175560.1 362 LDQWDIARnpsaevqtfyragpagvpsqvafsqstrwpsldtdR--AegCIRSGEHAFSQEGGLAVLVG 428
                                               *******99******************************66444..156******************** PP

                                 TIGR00110 369 nlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPt 437
                                               n+a +G+vvk+agv++ +l+feG+a+v es++ea++ il+ kvk+Gdvv++ryeGPkGgPGm+emL+Pt
  lcl|NCBI__GCF_001592305.1:WP_068175560.1 429 NIALNGCVVKTAGVDDALLVFEGTAHVTESQDEAVANILDDKVKAGDVVIVRYEGPKGGPGMQEMLYPT 497
                                               ********************************************************************* PP

                                 TIGR00110 438 salvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeel 506
                                               s++++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv++GD+i+iDi+nr +++ vs++el
  lcl|NCBI__GCF_001592305.1:WP_068175560.1 498 SYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIGLVRNGDRIRIDIPNRSINVLVSDDEL 566
                                               ********************************************************************* PP

                                 TIGR00110 507 aerrakakkkea.......revkgaLakyaklvssadkGavld 542
                                               a+rr ++++k++       r+v+ aL++ya l+ sadkGav+d
  lcl|NCBI__GCF_001592305.1:WP_068175560.1 567 AQRRSEQDAKGWkpalprkRKVSAALKAYALLAMSADKGAVRD 609
                                               ************9****9999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (615 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: 11.77
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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