Alignments for a candidate for ilvD in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Shewanella sp. ANA-3

Align dihydroxyacid dehydratase (characterized)
to candidate 7023120 Shewana3_0358 dihydroxy-acid dehydratase (RefSeq)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__ANA3:7023120
          Length = 619

 Score =  983 bits (2540), Expect = 0.0
 Identities = 493/617 (79%), Positives = 543/617 (88%), Gaps = 3/617 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MPK RSAT+T GRNMAGARALWRATG+ D DFGKPIIA+ NSFTQFVPGHVHL+D+G LV
Sbjct: 1   MPKLRSATSTEGRNMAGARALWRATGVKDNDFGKPIIAIANSFTQFVPGHVHLKDMGSLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A+ IE AGG+AKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADA+VCIS
Sbjct: 61  ADAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMA+LRLNIPV+FVSGGPMEAGKTKLSD++IKLDLVDAM+  AD  VSD  
Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADSSVSDED 180

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           S ++ERSACPTCGSCSGMFTANSMNCLTEALGLS PGNGS+LATHADR++LFL AG+R++
Sbjct: 181 SAKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRRVM 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
            LTKRYYEQ+D SALPRNIAS  AFENAM LDIAMGGS+NTVLHLLAAAQEA++ FTM D
Sbjct: 241 ALTKRYYEQDDASALPRNIASFKAFENAMALDIAMGGSSNTVLHLLAAAQEADVAFTMDD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNV---LGLTL 357
           ID++SR+VP LCKVAPST KYHMEDVHRAGGV+GILGELDRAGLL+ DV +V    G  L
Sbjct: 301 IDRMSRQVPHLCKVAPSTAKYHMEDVHRAGGVMGILGELDRAGLLHTDVPHVAADAGGNL 360

Query: 358 PQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYS 417
              L +YDVM TQDD VK  F AGPAGI TT+AFSQDCRW +LDDDR  GCIRS E A+S
Sbjct: 361 KSVLAKYDVMQTQDDKVKQFFMAGPAGIPTTKAFSQDCRWPSLDDDRREGCIRSREFAFS 420

Query: 418 KDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVV 477
           ++GGLAVL GN A+NGCIVKTAGVD+S L F G A+VYESQDDAV  ILGG+VVAGDVVV
Sbjct: 421 QEGGLAVLSGNLADNGCIVKTAGVDESNLTFIGSARVYESQDDAVAGILGGEVVAGDVVV 480

Query: 478 IRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGS 537
           IRYEGPKGGPGMQEMLYPTS+LKS GLGKACALITDGRFSGGTSGLSIGHVSPEAA+GG+
Sbjct: 481 IRYEGPKGGPGMQEMLYPTSYLKSRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGT 540

Query: 538 IGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYA 597
           I LIE+GD I IDIP R I+L VSDAELAARRE   ARG  AW P +R+R VS AL+AYA
Sbjct: 541 IALIENGDRIEIDIPKRSIKLAVSDAELAARRETMLARGPMAWKPLSRQRYVSMALKAYA 600

Query: 598 SLATSADKGAVRDKSKL 614
            LATSADKGAVRD+SKL
Sbjct: 601 MLATSADKGAVRDRSKL 617


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: 1306
Number of extensions: 49
Number of successful extensions: 2
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: 619
Length adjustment: 37
Effective length of query: 579
Effective length of database: 582
Effective search space:   336978
Effective search space used:   336978
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 7023120 Shewana3_0358 (dihydroxy-acid dehydratase (RefSeq))
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.12355.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.5e-258  844.0   4.1   2.9e-258  843.8   4.1    1.0  1  lcl|FitnessBrowser__ANA3:7023120  Shewana3_0358 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023120  Shewana3_0358 dihydroxy-acid dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  843.8   4.1  2.9e-258  2.9e-258       2     542 ..      18     613 ..      17     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: 843.8 bits;  conditional E-value: 2.9e-258
                         TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysL 78 
                                       aral++atG+kd+d++kPiia++ns+t++vPghvhlkd+++lv+++ie+aGg+akefntiav+DGiamgh+Gm+ysL
  lcl|FitnessBrowser__ANA3:7023120  18 ARALWRATGVKDNDFGKPIIAIANSFTQFVPGHVHLKDMGSLVADAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSL 94 
                                       79*************************************************************************** PP

                         TIGR00110  79 psreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgey 155
                                       psre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkls+k++++d+++a++++
  lcl|FitnessBrowser__ANA3:7023120  95 PSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAA 171
                                       ***************************************************************************** PP

                         TIGR00110 156 aagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik 232
                                       a++ +s+e++ +iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a+++el+ ++g+r++ l+k++++
  lcl|FitnessBrowser__ANA3:7023120 172 ADSSVSDEDSAKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRRVMALTKRYYE 248
                                       ***************************************************************************** PP

                         TIGR00110 233 .......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.ied 301
                                              Pr+i++ +afena++ld+a+GGs+ntvLhlla+a+ea+v +++dd+dr+sr+vP+l+k++Ps+ k+ +ed
  lcl|FitnessBrowser__ANA3:7023120 249 qddasalPRNIASFKAFENAMALDIAMGGSSNTVLHLLAAAQEADVAFTMDDIDRMSRQVPHLCKVAPSTAKYhMED 325
                                       **********************************************************************9999*** PP

                         TIGR00110 302 lhraGGvsavlkeldkegllhkdaltvt...Gktlaetlekvkvlr............................... 344
                                       +hraGGv+++l+eld++gllh+d+  v+   G  l+ +l+k++v++                               
  lcl|FitnessBrowser__ANA3:7023120 326 VHRAGGVMGILGELDRAGLLHTDVPHVAadaGGNLKSVLAKYDVMQtqddkvkqffmagpagipttkafsqdcrwps 402
                                       ***********************99985333889***********9******************************9 PP

                         TIGR00110 345 vdqd....virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvv 417
                                       +d+d    +irs + ++++egglavL Gnla++G++vk+agv+e+ l+f G+a+v+es+++a+++ilgg+v +Gdvv
  lcl|FitnessBrowser__ANA3:7023120 403 LDDDrregCIRSREFAFSQEGGLAVLSGNLADNGCIVKTAGVDESNLTFIGSARVYESQDDAVAGILGGEVVAGDVV 479
                                       44444566********************************************************************* PP

                         TIGR00110 418 viryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDien 494
                                       viryeGPkGgPGm+emL+Pts+l++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaa+gG+ial+e+GD+i+iDi++
  lcl|FitnessBrowser__ANA3:7023120 480 VIRYEGPKGGPGMQEMLYPTSYLKSRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGTIALIENGDRIEIDIPK 556
                                       ***************************************************************************** PP

                         TIGR00110 495 rkldlevseeelaerrakakkkea.........revkgaLakyaklvssadkGavld 542
                                       r ++l+vs++ela+rr+++ ++++         r+v+ aL++ya l++sadkGav+d
  lcl|FitnessBrowser__ANA3:7023120 557 RSIKLAVSDAELAARRETMLARGPmawkplsrqRYVSMALKAYAMLATSADKGAVRD 613
                                       **********************9999*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (619 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: 11.95
//
[ok]

This GapMind analysis is from Apr 09 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