Alignments for a candidate for ilvD in Phaeobacter inhibens BS107

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.7086.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: 0.02u 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