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.21805.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.93
//
[ok]

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

Links

Downloads

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:

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:

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:

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:

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