Alignments for a candidate for ilvD in Synechococcus elongatus PCC 7942

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.23011.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.39
//
[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