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 dihydroxyacid dehydratase (characterized)
to candidate WP_086509434.1 BZY95_RS08080 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_002151265.1:WP_086509434.1
          Length = 614

 Score =  933 bits (2412), Expect = 0.0
 Identities = 468/615 (76%), Positives = 528/615 (85%), Gaps = 3/615 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP+YRS TTT GRNMAGARALWRATGM D DF KPIIAV NSFTQFVPGHVHL+D+G+LV
Sbjct: 1   MPQYRSRTTTAGRNMAGARALWRATGMKDEDFHKPIIAVANSFTQFVPGHVHLKDMGQLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A +IE AGGVAKEFNTIAVDDGIAMGH GMLYSLPSR++IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIEKAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMA++RLNIPVIFVSGGPMEAGKTKL D    LDLVDAM+  AD  V D  
Sbjct: 121 NCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKTKLLDH--GLDLVDAMVMAADDSVDDET 178

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
             +VERSACPTCGSCSGMFTANSMNCLTEALGL+ PGNG++LATHADR++LF  AG RIV
Sbjct: 179 LAEVERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGTVLATHADRRRLFETAGHRIV 238

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           EL KRYYE ++   LPR I SKAAF+NAMTLDIAMGGSTNT+LHLLAAAQEAEIDFTM+D
Sbjct: 239 ELAKRYYEGDEAHLLPRAIGSKAAFKNAMTLDIAMGGSTNTILHLLAAAQEAEIDFTMAD 298

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           ID+LSR+VPQLCKVAP+TQKYH+EDVHRAGG++ ILGELDRAG+L+  V  V G +L + 
Sbjct: 299 IDRLSREVPQLCKVAPNTQKYHIEDVHRAGGIMAILGELDRAGVLDTRVPTVYGDSLKEA 358

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           L+++D+M      V   F+AGP G+ T  AFSQ  RW TLD DRANGCIR LEHA+S++G
Sbjct: 359 LDEWDIMRNPSPEVVEFFKAGPGGVPTQVAFSQSARWPTLDGDRANGCIRDLEHAFSREG 418

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVLYGN A +GC+VKTAGVDDSIL F GPA V ESQD AVE IL G+V  G+VVVIRY
Sbjct: 419 GLAVLYGNIAVDGCVVKTAGVDDSILVFEGPAHVVESQDQAVEHILAGQVKEGEVVVIRY 478

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPTS+LKS GLGKACAL+TDGRFSGGTSGLSIGHVSPEAA+GG+IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAAGGAIGL 538

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPK-NRERQVSFALRAYASL 599
           +  GD+I IDIPNR I +++SD+ELAARREA++ARG +AW P   R R+VS AL+AYA L
Sbjct: 539 VRSGDIIRIDIPNRRIDVKLSDSELAARREAEEARGSQAWKPSIQRVRKVSAALKAYALL 598

Query: 600 ATSADKGAVRDKSKL 614
           ATSADKGAVRD SKL
Sbjct: 599 ATSADKGAVRDLSKL 613


Lambda     K      H
   0.317    0.134    0.386 

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: 1243
Number of extensions: 40
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: 616
Length of database: 614
Length adjustment: 37
Effective length of query: 579
Effective length of database: 577
Effective search space:   334083
Effective search space used:   334083
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_086509434.1 BZY95_RS08080 (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.15549.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-259  847.7   2.2   2.1e-259  847.5   2.2    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509434.1  BZY95_RS08080 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509434.1  BZY95_RS08080 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  847.5   2.2  2.1e-259  2.1e-259       2     542 ..      18     609 ..      17     610 .. 0.98

  Alignments for each domain:
  == domain 1  score: 847.5 bits;  conditional E-value: 2.1e-259
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG+kded++kPiiav+ns+t++vPghvhlkd+++lv++eie+aGgvakefntiav+DGiamg
  lcl|NCBI__GCF_002151265.1:WP_086509434.1  18 ARALWRATGMKDEDFHKPIIAVANSFTQFVPGHVHLKDMGQLVAREIEKAGGVAKEFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsr+iiaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpmeagktkl
  lcl|NCBI__GCF_002151265.1:WP_086509434.1  87 HDGMLYSLPSRDIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKTKL 155
                                               ********************************************************************8 PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                                +  + +d+++a++++a++ +++e+l e+ersacPt+gsCsG+ftansm+cltealGl+lPg++t+lat
  lcl|NCBI__GCF_002151265.1:WP_086509434.1 156 LD--HGLDLVDAMVMAADDSVDDETLAEVERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGTVLAT 222
                                               44..4699************************************************************* PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +a++++l++++g+rivel k++++       Pr i +k+af+na+tld+a+GGstnt+Lhlla+a+ea+
  lcl|NCBI__GCF_002151265.1:WP_086509434.1 223 HADRRRLFETAGHRIVELAKRYYEgdeahllPRAIGSKAAFKNAMTLDIAMGGSTNTILHLLAAAQEAE 291
                                               ********************************************************************* PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338
                                               +++++ d+drlsr+vP+l+k++P+++k+ ied+hraGG++a+l+eld++g+l++ + tv G++l+e l+
  lcl|NCBI__GCF_002151265.1:WP_086509434.1 292 IDFTMADIDRLSREVPQLCKVAPNTQKYhIEDVHRAGGIMAILGELDRAGVLDTRVPTVYGDSLKEALD 360
                                               ***************************99**************************************** PP

                                 TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372
                                               + +++r                                     + +ir l++++++egglavL+Gn+a 
  lcl|NCBI__GCF_002151265.1:WP_086509434.1 361 EWDIMRnpspevveffkagpggvptqvafsqsarwptldgdRANGCIRDLEHAFSREGGLAVLYGNIAV 429
                                               *************************************87666666************************ PP

                                 TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441
                                               +G+vvk+agv+++il+feGpa+v es+++a+e il+g+vkeG+vvviryeGPkGgPGm+emL+Pts+l+
  lcl|NCBI__GCF_002151265.1:WP_086509434.1 430 DGCVVKTAGVDDSILVFEGPAHVVESQDQAVEHILAGQVKEGEVVVIRYEGPKGGPGMQEMLYPTSYLK 498
                                               ********************************************************************* PP

                                 TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                               + GLgk++aL+tDGrfsGgt+GlsiGhvsPeaa+gGai+lv+ GD+i+iDi+nr++d+++s+ ela+rr
  lcl|NCBI__GCF_002151265.1:WP_086509434.1 499 SKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAAGGAIGLVRSGDIIRIDIPNRRIDVKLSDSELAARR 567
                                               ********************************************************************* PP

                                 TIGR00110 511 akakkkea..........revkgaLakyaklvssadkGavld 542
                                               ++ ++++           r+v+ aL++ya l++sadkGav+d
  lcl|NCBI__GCF_002151265.1:WP_086509434.1 568 EAEEARGSqawkpsiqrvRKVSAALKAYALLATSADKGAVRD 609
                                               ***99999999*******9*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (614 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: 11.89
//
[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