GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Shewanella amazonensis SB2B

Align dihydroxyacid dehydratase (characterized)
to candidate 6939185 Sama_3279 dihydroxy-acid dehydratase (RefSeq)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__SB2B:6939185
          Length = 618

 Score =  971 bits (2510), Expect = 0.0
 Identities = 484/618 (78%), Positives = 543/618 (87%), Gaps = 2/618 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           M K RSAT+T GRNMAGARALWRATG+ D DFGKPIIA+ NSFTQFVPGHVHL+D+G LV
Sbjct: 1   MAKLRSATSTEGRNMAGARALWRATGVKDTDFGKPIIAIANSFTQFVPGHVHLKDMGSLV 60

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

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMA+LRLNIPV+FVSGGPMEAGKTKLSD++IKLDLVDAM+  AD ++SD+ 
Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADDRISDAD 180

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

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           +L KRYY  +D S LPR+IAS  AFENAM LD+AMGGS+NTVLHLLAAAQEAE+DFTM D
Sbjct: 241 KLAKRYYGDDDASVLPRSIASFKAFENAMALDVAMGGSSNTVLHLLAAAQEAEVDFTMDD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGL--TLP 358
           ID++SRKVP LCKVAPST KYHMEDVHRAGGV+ ILGELDRAGLL+ DV +V     TL 
Sbjct: 301 IDRISRKVPHLCKVAPSTPKYHMEDVHRAGGVMAILGELDRAGLLHTDVNHVASEDGTLK 360

Query: 359 QTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSK 418
             LE++DV+LT+D+ V   FRAGPAGI TT+AFSQ CRWDTLDDDR  GCIRS E A+S+
Sbjct: 361 SVLERFDVVLTKDEKVHEFFRAGPAGIPTTRAFSQSCRWDTLDDDRREGCIRSREFAFSQ 420

Query: 419 DGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVI 478
           +GGLAVL GN AENGCIVKTAGVD+S LKF+G A+VYESQ+DAV  ILGG+VVAGDVVVI
Sbjct: 421 EGGLAVLSGNLAENGCIVKTAGVDESNLKFSGVARVYESQEDAVAGILGGEVVAGDVVVI 480

Query: 479 RYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSI 538
           R+EGPKGGPGMQEMLYPTS+LKS GLG  CALITDGRFSGGTSGLSIGHVSPEAASGG+I
Sbjct: 481 RFEGPKGGPGMQEMLYPTSYLKSRGLGTQCALITDGRFSGGTSGLSIGHVSPEAASGGTI 540

Query: 539 GLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYAS 598
           GLIE+GD I IDIP R I+L VSDAEL +RR A +A+G  AW P +R R VS AL+AYA 
Sbjct: 541 GLIENGDRIDIDIPGRSIKLLVSDAELESRRAAMNAKGPLAWKPLSRVRPVSMALKAYAM 600

Query: 599 LATSADKGAVRDKSKLGG 616
           LATSADKGAVRD SKL G
Sbjct: 601 LATSADKGAVRDVSKLEG 618


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: 1274
Number of extensions: 51
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: 618
Length adjustment: 37
Effective length of query: 579
Effective length of database: 581
Effective search space:   336399
Effective search space used:   336399
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 6939185 Sama_3279 (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.13586.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-257  840.5   2.2   3.3e-257  840.3   2.2    1.0  1  lcl|FitnessBrowser__SB2B:6939185  Sama_3279 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939185  Sama_3279 dihydroxy-acid dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  840.3   2.2  3.3e-257  3.3e-257       2     542 ..      18     612 ..      17     613 .. 0.98

  Alignments for each domain:
  == domain 1  score: 840.3 bits;  conditional E-value: 3.3e-257
                         TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysL 78 
                                       aral++atG+kd d++kPiia++ns+t++vPghvhlkd+++lv+ +ie+aGg+akefntiav+DGiamgh+Gm+ysL
  lcl|FitnessBrowser__SB2B:6939185  18 ARALWRATGVKDTDFGKPIIAIANSFTQFVPGHVHLKDMGSLVASAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSL 94 
                                       79*************************************************************************** PP

                         TIGR00110  79 psreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgey 155
                                       psre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkls+k++++d+++a++++
  lcl|FitnessBrowser__SB2B:6939185  95 PSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAA 171
                                       ***************************************************************************** PP

                         TIGR00110 156 aagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik 232
                                       a++++s++++e+iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a+++el+ ++g+r+++l k+++ 
  lcl|FitnessBrowser__SB2B:6939185 172 ADDRISDADSEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSMLATHADRRELFLEAGRRVMKLAKRYYG 248
                                       ****************************************************************************9 PP

                         TIGR00110 233 .......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.ied 301
                                              Pr+i++ +afena++ld+a+GGs+ntvLhlla+a+ea+v++++dd+dr+srkvP+l+k++Ps+ k+ +ed
  lcl|FitnessBrowser__SB2B:6939185 249 dddasvlPRSIASFKAFENAMALDVAMGGSSNTVLHLLAAAQEAEVDFTMDDIDRISRKVPHLCKVAPSTPKYhMED 325
                                       9999******************************************************************9999*** PP

                         TIGR00110 302 lhraGGvsavlkeldkegllhkdaltvtGk..tlaetlekvkvlr...............................v 345
                                       +hraGGv+a+l+eld++gllh+d+  v+ +  tl+ +le+ +v                                 +
  lcl|FitnessBrowser__SB2B:6939185 326 VHRAGGVMAILGELDRAGLLHTDVNHVASEdgTLKSVLERFDVVLtkdekvheffragpagipttrafsqscrwdtL 402
                                       *************************99875559*********99999****************************94 PP

                         TIGR00110 346 dqd....virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvv 418
                                       d+d    +irs + ++++egglavL Gnlae+G++vk+agv+e+ lkf G a+v+es+e+a+++ilgg+v +Gdvvv
  lcl|FitnessBrowser__SB2B:6939185 403 DDDrregCIRSREFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLKFSGVARVYESQEDAVAGILGGEVVAGDVVV 479
                                       4444566********************************************************************** PP

                         TIGR00110 419 iryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienr 495
                                       ir+eGPkGgPGm+emL+Pts+l++ GLg ++aLitDGrfsGgt+GlsiGhvsPeaa+gG+i+l+e+GD+i iDi+ r
  lcl|FitnessBrowser__SB2B:6939185 480 IRFEGPKGGPGMQEMLYPTSYLKSRGLGTQCALITDGRFSGGTSGLSIGHVSPEAASGGTIGLIENGDRIDIDIPGR 556
                                       ***************************************************************************** PP

                         TIGR00110 496 kldlevseeelaerrakakkkea.........revkgaLakyaklvssadkGavld 542
                                        ++l vs++el++rra++++k++         r v+ aL++ya l++sadkGav+d
  lcl|FitnessBrowser__SB2B:6939185 557 SIKLLVSDAELESRRAAMNAKGPlawkplsrvRPVSMALKAYAMLATSADKGAVRD 612
                                       ******************************9999********************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.99
//
[ok]

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

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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