Alignments for a candidate for ilvD in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Shewanella oneidensis MR-1

Align dihydroxyacid dehydratase (characterized)
to candidate 203423 SO4345 dihydroxy-acid dehydratase (NCBI ptt file)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__MR1:203423
          Length = 619

 Score =  974 bits (2519), Expect = 0.0
 Identities = 492/617 (79%), Positives = 537/617 (87%), 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  ASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120

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

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           S ++ERSACPTCGSCSGMFTANSMNCLTEALGLS PGNGS+LATH+DR++LFL AG+R++
Sbjct: 181 SAKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHSDRRELFLEAGRRVM 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
            LTKRYYEQ+D SALPRNIA   AFENA  LDIAMGGS+NTVLHLLAAAQEAE+ FTM D
Sbjct: 241 ALTKRYYEQDDTSALPRNIACFKAFENATALDIAMGGSSNTVLHLLAAAQEAEVAFTMDD 300

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

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

Query: 418 KDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVV 477
           ++GGLAVL GN AENGCIVKTAGVD+S L F G A+VYESQDDAV  ILGG+VVAGDVVV
Sbjct: 421 QEGGLAVLSGNLAENGCIVKTAGVDESNLIFVGSARVYESQDDAVAGILGGEVVAGDVVV 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 VSDAELA RRE   ARG  AW P  RER VS AL+AYA
Sbjct: 541 IALIENGDRIEIDIPARSIKLAVSDAELAGRRETMLARGPMAWKPVGRERFVSMALKAYA 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: 1291
Number of extensions: 44
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 203423 SO4345 (dihydroxy-acid dehydratase (NCBI ptt file))
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.12414.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     3e-255  833.8   3.6   3.5e-255  833.6   3.6    1.0  1  lcl|FitnessBrowser__MR1:203423  SO4345 dihydroxy-acid dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203423  SO4345 dihydroxy-acid dehydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  833.6   3.6  3.5e-255  3.5e-255       2     542 ..      18     613 ..      17     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: 833.6 bits;  conditional E-value: 3.5e-255
                       TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysLps 80 
                                     aral++atG+kd+d++kPiia++ns+t++vPghvhlkd+++lv+ +ie+aGg+akefntiav+DGiamgh+Gm+ysLps
  lcl|FitnessBrowser__MR1:203423  18 ARALWRATGVKDNDFGKPIIAIANSFTQFVPGHVHLKDMGSLVASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPS 96 
                                     79***************************************************************************** PP

                       TIGR00110  81 reiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgeyaagk 159
                                     re+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkls+k++++d+++a++++a++ 
  lcl|FitnessBrowser__MR1:203423  97 RELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADSS 175
                                     ******************************************************************************* PP

                       TIGR00110 160 lseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik...... 232
                                     +s+e++ +iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+++++el+ ++g+r++ l+k++++      
  lcl|FitnessBrowser__MR1:203423 176 VSDEDSAKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHSDRRELFLEAGRRVMALTKRYYEqddtsa 254
                                     ******************************************************************************* PP

                       TIGR00110 233 .PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvs 309
                                      Pr+i+  +afena +ld+a+GGs+ntvLhlla+a+ea+v +++dd+dr+sr vP+l+k++Ps+ k+ +ed+hraGGv+
  lcl|FitnessBrowser__MR1:203423 255 lPRNIACFKAFENATALDIAMGGSSNTVLHLLAAAQEAEVAFTMDDIDRMSRLVPHLCKVAPSTPKYhMEDVHRAGGVM 333
                                     ****************************************************************9999*********** PP

                       TIGR00110 310 avlkeldkegllhkdaltvt...Gktlaetlekvkvlr...............................vdqd....vi 350
                                     ++l+eld++gllh+d+  v+   G  l+ +l+k++v++                               +d+d    +i
  lcl|FitnessBrowser__MR1:203423 334 GILGELDRAGLLHTDVPHVAadaGGNLKSVLAKYDVMQtqddnvkqffmagpagipttkafsqdcrwpsLDDDrregCI 412
                                     ***************99985333889***********9******************************944444566** PP

                       TIGR00110 351 rsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPG 429
                                     rs + ++++egglavL Gnlae+G++vk+agv+e+ l f G+a+v+es+++a+++ilgg+v +GdvvviryeGPkGgPG
  lcl|FitnessBrowser__MR1:203423 413 RSREFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLIFVGSARVYESQDDAVAGILGGEVVAGDVVVIRYEGPKGGPG 491
                                     ******************************************************************************* PP

                       TIGR00110 430 mremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508
                                     m+emL+Pts+l++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaa+gG+ial+e+GD+i+iDi++r ++l+vs++ela 
  lcl|FitnessBrowser__MR1:203423 492 MQEMLYPTSYLKSRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGTIALIENGDRIEIDIPARSIKLAVSDAELAG 570
                                     ******************************************************************************* PP

                       TIGR00110 509 rrakakkkea.........revkgaLakyaklvssadkGavld 542
                                     rr+++ ++++         r v+ aL++ya l++sadkGav+d
  lcl|FitnessBrowser__MR1:203423 571 RRETMLARGPmawkpvgreRFVSMALKAYAMLATSADKGAVRD 613
                                     ********9999*****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: 12.90
//
[ok]

This GapMind analysis is from Apr 09 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