GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Phaeobacter inhibens BS107

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate GFF2902 PGA1_c29490 dihydroxy-acid dehydratase LivD

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__Phaeo:GFF2902
          Length = 614

 Score =  926 bits (2394), Expect = 0.0
 Identities = 461/610 (75%), Positives = 522/610 (85%), Gaps = 1/610 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP+YRSRT+THGRNMAGARGLWRATGM D DFGKPIIA+VNSFTQFVPGHVHLKDLGQ+V
Sbjct: 1   MPMYRSRTSTHGRNMAGARGLWRATGMTDDDFGKPIIAIVNSFTQFVPGHVHLKDLGQMV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           ARE+EAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREVEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREVIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKV-VMHGKTHALDLVDAMVAAADDKISDE 179
           NCDKITPGMLMA++RLNIP +FVSGGPMEAGK+ +       +DLVDAMVAAA D ++DE
Sbjct: 121 NCDKITPGMLMAAMRLNIPAIFVSGGPMEAGKIDIADLDMKKIDLVDAMVAAASDTMTDE 180

Query: 180 DVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLI 239
            VQ IE +ACPTCGSCSGMFTANSMNCL EALGL+LPGNGSTLATH DRK LF+EAG  I
Sbjct: 181 QVQHIEENACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHADRKHLFLEAGRKI 240

Query: 240 VDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMA 299
           VD+ +R+Y  ++   LPR IA+  AFENAM+LDIAMGGSTNTVLH+LA A+EG++DFTM 
Sbjct: 241 VDITKRHYVGEEKGLLPREIATFDAFENAMSLDIAMGGSTNTVLHLLAIANEGKVDFTMT 300

Query: 300 DIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGD 359
           D+D LSR+VPCL KVAP   +VHMEDVHRAGGI SILGEL + GLL+ +C TVH+ T+G+
Sbjct: 301 DMDRLSRKVPCLCKVAPNIENVHMEDVHRAGGIFSILGELSRAGLLHNECSTVHSSTMGE 360

Query: 360 AIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKD 419
           AI +WDI   N+      ++AAPGG+ T  AFSQ  R+ ELDTDRE GVIRS +H FS+D
Sbjct: 361 AIAKWDIKVANNPDAEALFKAAPGGVRTTEAFSQSNRYKELDTDREGGVIRSKDHAFSQD 420

Query: 420 GGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIR 479
           GGLAVL GN+A DGCIVKTAGVD++ILKF+G A V ESQD +V  IL ++VK GDVVVIR
Sbjct: 421 GGLAVLFGNIARDGCIVKTAGVDDNILKFTGSAYVCESQDQAVNDILTSKVKEGDVVVIR 480

Query: 480 YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIG 539
           YEGP+GGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGH SPEAA GGTIG
Sbjct: 481 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGTIG 540

Query: 540 LVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFAT 599
           LV++GD I+IDIPNRTI L VS+ ELAARRA QDA GW P + RKR V+TALKAYA  AT
Sbjct: 541 LVQQGDTIEIDIPNRTIHLAVSDEELAARRAAQDAAGWKPVKPRKRKVSTALKAYALLAT 600

Query: 600 SADRGAVRDL 609
           SA +GAVR L
Sbjct: 601 SAAKGAVRAL 610


Lambda     K      H
   0.318    0.134    0.391 

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: 1211
Number of extensions: 29
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: 612
Length of database: 614
Length adjustment: 37
Effective length of query: 575
Effective length of database: 577
Effective search space:   331775
Effective search space used:   331775
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 GFF2902 PGA1_c29490 (dihydroxy-acid dehydratase LivD)
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.3537.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.2e-257  839.6   7.8     6e-257  839.4   7.8    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2902  PGA1_c29490 dihydroxy-acid dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2902  PGA1_c29490 dihydroxy-acid dehydratase LivD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  839.4   7.8    6e-257    6e-257       2     541 ..      18     608 ..      17     610 .. 0.98

  Alignments for each domain:
  == domain 1  score: 839.4 bits;  conditional E-value: 6e-257
                          TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 
                                        ar l++atG++d+d++kPiia+vns+t++vPghvhlkdl+++v++e+eaaGgvakefntiav+DGiamgh+Gm+ys
  lcl|FitnessBrowser__Phaeo:GFF2902  18 ARGLWRATGMTDDDFGKPIIAIVNSFTQFVPGHVHLKDLGQMVAREVEAAGGVAKEFNTIAVDDGIAMGHDGMLYS 93 
                                        689************************************************************************* PP

                          TIGR00110  78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklse.kidlvdvfeav 152
                                        Lpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniPai+vsGGpmeagk+ +++ +++++d+++a+
  lcl|FitnessBrowser__Phaeo:GFF2902  94 LPSREVIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAIFVSGGPMEAGKIDIADlDMKKIDLVDAM 169
                                        *************************************************************97658999******* PP

                          TIGR00110 153 geyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvk 228
                                        +++a++ +++e++++ie++acPt+gsCsG+ftansm+cl+ealGl+lPg++++lat+a++k+l+ ++g++iv+++k
  lcl|FitnessBrowser__Phaeo:GFF2902 170 VAAASDTMTDEQVQHIEENACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHADRKHLFLEAGRKIVDITK 245
                                        **************************************************************************** PP

                          TIGR00110 229 knik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkk 297
                                        +++        Pr+i+t +afena++ld+a+GGstntvLhllaia+e +v++++ d+drlsrkvP+l+k++P+ ++
  lcl|FitnessBrowser__Phaeo:GFF2902 246 RHYVgeekgllPREIATFDAFENAMSLDIAMGGSTNTVLHLLAIANEGKVDFTMTDMDRLSRKVPCLCKVAPNIEN 321
                                        **999999******************************************************************99 PP

                          TIGR00110 298 v.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............................ 344
                                        v +ed+hraGG+ ++l+el+++gllh+++ tv  +t++e ++k +++                             
  lcl|FitnessBrowser__Phaeo:GFF2902 322 VhMEDVHRAGGIFSILGELSRAGLLHNECSTVHSSTMGEAIAKWDIKVannpdaealfkaapggvrtteafsqsnr 397
                                        99*******************************************99999************************** PP

                          TIGR00110 345 .....vdqd..virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                             +d++  virs+d++++++gglavL+Gn+a +G++vk+agv+++ilkf+G+a v es+++a++ il+ kvke
  lcl|FitnessBrowser__Phaeo:GFF2902 398 ykeldTDREggVIRSKDHAFSQDGGLAVLFGNIARDGCIVKTAGVDDNILKFTGSAYVCESQDQAVNDILTSKVKE 473
                                        *9966444477***************************************************************** PP

                          TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkik 489
                                        GdvvviryeGP+GgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGhvsPeaaegG+i+lv++GD+i+
  lcl|FitnessBrowser__Phaeo:GFF2902 474 GDVVVIRYEGPRGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGTIGLVQQGDTIE 549
                                        **************************************************************************** PP

                          TIGR00110 490 iDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavl 541
                                        iDi+nr+++l+vs+eela+rra++++ ++       r+v+ aL++ya l++sa kGav+
  lcl|FitnessBrowser__Phaeo:GFF2902 550 IDIPNRTIHLAVSDEELAARRAAQDAAGWkpvkprkRKVSTALKAYALLATSAAKGAVR 608
                                        *************************9999999999999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (614 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: 8.16
//
[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