GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Synechococcus elongatus PCC 7942

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>FitnessBrowser__SynE:Synpcc7942_0626
          Length = 619

 Score =  934 bits (2415), Expect = 0.0
 Identities = 473/615 (76%), Positives = 526/615 (85%), Gaps = 1/615 (0%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP YRSRTTT+GRNMAGAR LWRATGMKDEDF KPIIAVANSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPQYRSRTTTYGRNMAGARALWRATGMKDEDFEKPIIAVANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIE AGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIERAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180
           NCDKITPGMLMAA+RLNIP VFVSGGPMEAGKV + G+ R LDLVDAMVVAADD  SDE+
Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVILNGEERHLDLVDAMVVAADDRESDED 180

Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240
           V  IE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS+LATH DR+ LF EAGR+ V
Sbjct: 181 VATIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHGDRKELFLEAGRLAV 240

Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300
            L +++YEQ+D + LPR IA+  AFENA+ LDIAMGGSTNTVLHLLAAAHE G+DF+M D
Sbjct: 241 KLAKQYYEQDDESVLPRSIASFKAFENAICLDIAMGGSTNTVLHLLAAAHEAGVDFTMKD 300

Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360
           IDRLSR +P L KVAP+    HMEDVHRAGGV+AILGEL+R GL+    PTVH+P++G A
Sbjct: 301 IDRLSRKIPNLCKVAPSTQKYHMEDVHRAGGVIAILGELDRAGLLHREVPTVHSPSLGAA 360

Query: 361 LARWDIGR-TNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKD 419
           L +WDI R T ++ A   + AAPGG PTQ AFSQ+ RW  LDLDRENG IR +EH +S+D
Sbjct: 361 LDQWDINRETATEEAKSRYLAAPGGVPTQEAFSQSKRWTALDLDRENGCIRDIEHAYSQD 420

Query: 420 GGLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIR 479
           GGLAVL+GNLA +GCIVKTAGVDE+IL F G A V ESQD AV+ IL G+VK G+VV+IR
Sbjct: 421 GGLAVLYGNLAEQGCIVKTAGVDENILVFSGPAVVCESQDEAVNWILNGRVKEGDVVLIR 480

Query: 480 YEGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIA 539
           YEGP+GGPGMQEMLYPT+YLKSKGLG ACAL+TDGRFSGGTSGLSIGHVSPEA EGGLIA
Sbjct: 481 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIA 540

Query: 540 LVETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAM 599
           LVE GD I IDIP R I L VS+  LA RR A  ARG  AWTP +R R ++ AL+AYAAM
Sbjct: 541 LVEQGDRIEIDIPNRRIHLAVSEEELAHRRAAMEARGDQAWTPKDRDRPISQALQAYAAM 600

Query: 600 TTNAARGAVRDVSQI 614
           TT+AARG VRD+SQI
Sbjct: 601 TTSAARGGVRDLSQI 615


Lambda     K      H
   0.318    0.134    0.395 

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: 1297
Number of extensions: 42
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: 617
Length of database: 619
Length adjustment: 37
Effective length of query: 580
Effective length of database: 582
Effective search space:   337560
Effective search space used:   337560
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 Synpcc7942_0626 Synpcc7942_0626 (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.12989.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-254  829.4   0.3   7.6e-254  829.2   0.3    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0626  Synpcc7942_0626 dihydroxy-acid d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0626  Synpcc7942_0626 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  829.2   0.3  7.6e-254  7.6e-254       2     542 ..      18     611 ..      17     612 .. 0.99

  Alignments for each domain:
  == domain 1  score: 829.2 bits;  conditional E-value: 7.6e-254
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG+kded+ekPiiav+ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg
  lcl|FitnessBrowser__SynE:Synpcc7942_0626  18 ARALWRATGMKDEDFEKPIIAVANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniPa++vsGGpmeagk+ l
  lcl|FitnessBrowser__SynE:Synpcc7942_0626  87 HGGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVIL 155
                                               ********************************************************************* PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                                 +   +d+++a++ +a+++ s+e++ +iersacPt+gsCsG+ftansm+cltealGlslPg+++llat
  lcl|FitnessBrowser__SynE:Synpcc7942_0626 156 NGEERHLDLVDAMVVAADDRESDEDVATIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLAT 224
                                               99******************************************************************* PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               + ++kel+ ++g+  v+l k++++       Pr+i++ +afenai ld+a+GGstntvLhlla+a+eag
  lcl|FitnessBrowser__SynE:Synpcc7942_0626 225 HGDRKELFLEAGRLAVKLAKQYYEqddesvlPRSIASFKAFENAICLDIAMGGSTNTVLHLLAAAHEAG 293
                                               ********************************************************************* PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338
                                               v+++++d+drlsrk+P l+k++Ps++k+ +ed+hraGGv+a+l+eld++gllh+++ tv   +l+  l+
  lcl|FitnessBrowser__SynE:Synpcc7942_0626 294 VDFTMKDIDRLSRKIPNLCKVAPSTQKYhMEDVHRAGGVIAILGELDRAGLLHREVPTVHSPSLGAALD 362
                                               ***************************99**************************************** PP

                                 TIGR00110 339 kvkvlr....................................vdqdvirsldnpvkkegglavLkGnla 371
                                               + +++r                                     ++ +ir ++++++++gglavL+Gnla
  lcl|FitnessBrowser__SynE:Synpcc7942_0626 363 QWDINRetateeaksrylaapggvptqeafsqskrwtaldldRENGCIRDIEHAYSQDGGLAVLYGNLA 431
                                               *****9********************************99666666*********************** PP

                                 TIGR00110 372 eeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440
                                               e+G++vk+agv+e+il+f Gpa v es++ea++ il+g+vkeGdvv+iryeGP+GgPGm+emL+Pts+l
  lcl|FitnessBrowser__SynE:Synpcc7942_0626 432 EQGCIVKTAGVDENILVFSGPAVVCESQDEAVNWILNGRVKEGDVVLIRYEGPRGGPGMQEMLYPTSYL 500
                                               ********************************************************************* PP

                                 TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaer 509
                                               ++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG ialve+GD+i+iDi+nr+++l+vseeela+r
  lcl|FitnessBrowser__SynE:Synpcc7942_0626 501 KSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIALVEQGDRIEIDIPNRRIHLAVSEEELAHR 569
                                               ********************************************************************* PP

                                 TIGR00110 510 rakakkkea.........revkgaLakyaklvssadkGavld 542
                                               ra+++++++         r ++ aL++ya + +sa +G+v+d
  lcl|FitnessBrowser__SynE:Synpcc7942_0626 570 RAAMEARGDqawtpkdrdRPISQALQAYAAMTTSAARGGVRD 611
                                               ******999999***999999*******************87 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.33
//
[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:

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