Alignments for a candidate for ilvD in Thioalkalivibrio halophilus HL17

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Thioalkalivibrio halophilus HL17

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_077244832.1 B1A74_RS12665 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>NCBI__GCF_001995255.1:WP_077244832.1
          Length = 618

 Score =  958 bits (2477), Expect = 0.0
 Identities = 482/619 (77%), Positives = 534/619 (86%), Gaps = 3/619 (0%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP YRSRTTTHGRNMAGAR LWRATGMKD DF KPI+AVANSFTQFVPGHVHLKD+GQLV
Sbjct: 1   MPAYRSRTTTHGRNMAGARALWRATGMKDGDFDKPIVAVANSFTQFVPGHVHLKDMGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIE AGGVAKEFNTIAVDDGIAMGHGGMLYSLPSR++IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIEQAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGK--IRALDLVDAMVVAADDSYSD 178
           NCDKITPGML+AAMRLNIPVVFVSGGPMEAGKV   G+  +  LDLVDAMV AAD S SD
Sbjct: 121 NCDKITPGMLLAAMRLNIPVVFVSGGPMEAGKVQAPGQDNVIHLDLVDAMVKAADSSASD 180

Query: 179 EEVEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRV 238
           EEVEA+E++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS+LATHA R+ALF+EAGR 
Sbjct: 181 EEVEAVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHAARQALFEEAGRR 240

Query: 239 VVDLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSM 298
           VVDL +R+YEQ+DA+ALPR IAT  AFENAMSLDIAMGGSTNTVLHLLAAA EG +DF+M
Sbjct: 241 VVDLARRYYEQDDASALPRSIATFEAFENAMSLDIAMGGSTNTVLHLLAAAREGEVDFTM 300

Query: 299 ADIDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMG 358
           ADIDRLSRHVP L KVAPA    HMEDVHRAGGV+ IL EL+RGGLI    PTVHAPT+G
Sbjct: 301 ADIDRLSRHVPNLCKVAPATQQYHMEDVHRAGGVVGILAELDRGGLIHRDIPTVHAPTLG 360

Query: 359 EALARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSK 418
            AL +WD+ R  ++ +   + AAPGG PTQ AFSQ   W+ LDLDR +G IR +EH +S+
Sbjct: 361 AALEQWDVMRHAAE-SERLYSAAPGGVPTQTAFSQDRAWDSLDLDRASGCIRDIEHAYSQ 419

Query: 419 DGGLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVI 478
           DGGLAVL+GN+AP+GCIVKTAGVDESIL F G ARVFESQDAAV GILG QV+AG+VV+I
Sbjct: 420 DGGLAVLYGNMAPDGCIVKTAGVDESILKFSGPARVFESQDAAVEGILGDQVQAGDVVII 479

Query: 479 RYEGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLI 538
           RYEGPKGGPGMQEMLYPT+YLKSKGLG  CAL+TDGRFSGGTSGLSIGHVSPEA +GG I
Sbjct: 480 RYEGPKGGPGMQEMLYPTSYLKSKGLGKDCALITDGRFSGGTSGLSIGHVSPEAAQGGAI 539

Query: 539 ALVETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAA 598
            L+E GD I+IDIP R I ++V DA LAARREA  ARG  AW P +R R +T ALRAYA 
Sbjct: 540 GLIEEGDTIVIDIPAREIRIDVDDATLAARREAMEARGAKAWKPESRNRPVTQALRAYAL 599

Query: 599 MTTNAARGAVRDVSQIERG 617
           MTT+AA GAVRD+S +E G
Sbjct: 600 MTTSAAFGAVRDISPLEDG 618


Lambda     K      H
   0.318    0.134    0.395 

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: 1361
Number of extensions: 52
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: 617
Length of database: 618
Length adjustment: 37
Effective length of query: 580
Effective length of database: 581
Effective search space:   336980
Effective search space used:   336980
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_077244832.1 B1A74_RS12665 (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.6863.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-254  829.3   2.6     8e-254  829.1   2.6    1.0  1  lcl|NCBI__GCF_001995255.1:WP_077244832.1  B1A74_RS12665 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001995255.1:WP_077244832.1  B1A74_RS12665 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  829.1   2.6    8e-254    8e-254       2     542 ..      18     611 ..      17     612 .. 0.98

  Alignments for each domain:
  == domain 1  score: 829.1 bits;  conditional E-value: 8e-254
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG+kd d++kPi+av+ns+t++vPghvhlkd+++lv++eie+aGgvakefntiav+DGiamg
  lcl|NCBI__GCF_001995255.1:WP_077244832.1  18 ARALWRATGMKDGDFDKPIVAVANSFTQFVPGHVHLKDMGQLVAREIEQAGGVAKEFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsreiiaDsve++v+ah++Dalv+is+CDki+PGml+aa+rlniP+++vsGGpmeagk+++
  lcl|NCBI__GCF_001995255.1:WP_077244832.1  87 HGGMLYSLPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLLAAMRLNIPVVFVSGGPMEAGKVQA 155
                                               *******************************************************************98 PP

                                 TIGR00110 140 ..sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206
                                                  ++++ +d+++a++++a++  s+ee+e++ersacPt+gsCsG+ftansm+cltealGlslPg+++ll
  lcl|NCBI__GCF_001995255.1:WP_077244832.1 156 pgQDNVIHLDLVDAMVKAADSSASDEEVEAVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLL 224
                                               76799**************************************************************** PP

                                 TIGR00110 207 atsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiake 268
                                               at+a +++l++++g+r+v+l +++++       Pr+i+t eafena++ld+a+GGstntvLhlla+a+e
  lcl|NCBI__GCF_001995255.1:WP_077244832.1 225 ATHAARQALFEEAGRRVVDLARRYYEqddasalPRSIATFEAFENAMSLDIAMGGSTNTVLHLLAAARE 293
                                               ********************************************************************* PP

                                 TIGR00110 269 agvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaet 336
                                                +v++++ d+drlsr+vP l+k++P+++++ +ed+hraGGv ++l eld+ gl+h+d+ tv   tl+  
  lcl|NCBI__GCF_001995255.1:WP_077244832.1 294 GEVDFTMADIDRLSRHVPNLCKVAPATQQYhMEDVHRAGGVVGILAELDRGGLIHRDIPTVHAPTLGAA 362
                                               ****************************999************************************** PP

                                 TIGR00110 337 lekvkvlr..................................vdqdvirsldnpvkkegglavLkGnla 371
                                               le+ +v+r                                    + +ir ++++++++gglavL+Gn+a
  lcl|NCBI__GCF_001995255.1:WP_077244832.1 363 LEQWDVMRhaaeserlysaapggvptqtafsqdrawdsldldRASGCIRDIEHAYSQDGGLAVLYGNMA 431
                                               ***********************************99977544445*********************** PP

                                 TIGR00110 372 eeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440
                                               ++G++vk+agv+e+ilkf Gpa+vfes+++a+e+ilg +v++Gdvv+iryeGPkGgPGm+emL+Pts+l
  lcl|NCBI__GCF_001995255.1:WP_077244832.1 432 PDGCIVKTAGVDESILKFSGPARVFESQDAAVEGILGDQVQAGDVVIIRYEGPKGGPGMQEMLYPTSYL 500
                                               ********************************************************************* PP

                                 TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaer 509
                                               ++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaa+gGai+l+e+GD+i iDi++r++ ++v+++ la+r
  lcl|NCBI__GCF_001995255.1:WP_077244832.1 501 KSKGLGKDCALITDGRFSGGTSGLSIGHVSPEAAQGGAIGLIEEGDTIVIDIPAREIRIDVDDATLAAR 569
                                               ********************************************************************* PP

                                 TIGR00110 510 rakakkkea.........revkgaLakyaklvssadkGavld 542
                                               r+++++++a         r v  aL++ya + +sa  Gav+d
  lcl|NCBI__GCF_001995255.1:WP_077244832.1 570 REAMEARGAkawkpesrnRPVTQALRAYALMTTSAAFGAVRD 611
                                               *****9998899999999999*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (618 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 11.68
//
[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