Alignments for a candidate for ilvD in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pseudomonas stutzeri RCH2

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate GFF233 Psest_0234 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__psRCH2:GFF233
          Length = 612

 Score =  935 bits (2416), Expect = 0.0
 Identities = 462/608 (75%), Positives = 518/608 (85%), Gaps = 2/608 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRS+T+THGRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPDYRSKTSTHGRNMAGARALWRATGMKDEDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIE  GGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIEKHGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGMLMA+LRLNIP VFVSGGPMEAGK  +   +H LDLVDAMV AAD+  SDE 
Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKL--ASHGLDLVDAMVIAADESASDEK 178

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           V   ERSACPTCGSCSGMFTANSMNCL EALGL+LPGNGSTLATH DR++LF+ AG  +V
Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHSDREQLFLRAGRTVV 238

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
           +L +RYY + D   LPR IAS++AFENAMTLDIAMGGSTNT+LH+LAAA E E+DF +  
Sbjct: 239 ELCKRYYGEGDESVLPRNIASRRAFENAMTLDIAMGGSTNTILHLLAAAQEAEVDFDLRA 298

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           IDALSR+VP L KVAP     HMEDVHRAGGI SILGEL +GGLL+ D PTVH+ TL + 
Sbjct: 299 IDALSRKVPQLCKVAPNIQKYHMEDVHRAGGIFSILGELARGGLLHTDVPTVHSRTLAEG 358

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           I +WDIT+T  E V  F++A P GIPTQ AFSQ  RWD LD DRENG IRSVEH +S++G
Sbjct: 359 IAQWDITQTQDEAVHTFFKAGPAGIPTQTAFSQSTRWDSLDDDRENGCIRSVEHAYSQEG 418

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVL GN+A+DGC+VKTAGVDESI  F G A+++ESQD++VK ILA+EVKAGD+V+IRY
Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIYESQDSAVKGILADEVKAGDIVIIRY 478

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGPKGGPGMQEMLYPTSYLKSKGLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
           VR+GD + IDIPNR+I L+VS+ EL+ RR EQD KGW P + R R VTTALKAYA  ATS
Sbjct: 539 VRDGDKVLIDIPNRSIQLQVSDEELSHRRIEQDKKGWKPAQPRTRKVTTALKAYALLATS 598

Query: 601 ADRGAVRD 608
           AD+GAVR+
Sbjct: 599 ADKGAVRN 606


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: 1203
Number of extensions: 30
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: 612
Length adjustment: 37
Effective length of query: 575
Effective length of database: 575
Effective search space:   330625
Effective search space used:   330625
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 GFF233 Psest_0234 (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.30973.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     2e-255  834.4   1.3   2.3e-255  834.2   1.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF233  Psest_0234 dihydroxy-acid dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF233  Psest_0234 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  834.2   1.3  2.3e-255  2.3e-255       2     542 ..      18     606 ..      17     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: 834.2 bits;  conditional E-value: 2.3e-255
                          TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 
                                        aral++atG+kded++kPiia++ns+t++vPghvhlkdl++lv++eie+ Ggvakefntiav+DGiamgh+Gm+ys
  lcl|FitnessBrowser__psRCH2:GFF233  18 ARALWRATGMKDEDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKHGGVAKEFNTIAVDDGIAMGHDGMLYS 93 
                                        79************************************************************************** PP

                          TIGR00110  78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavg 153
                                        LpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkl    + +d+++a++
  lcl|FitnessBrowser__psRCH2:GFF233  94 LPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKL--ASHGLDLVDAMV 167
                                        *************************************************************8..557899****** PP

                          TIGR00110 154 eyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkk 229
                                         +a++  s+e++ e+ersacPt+gsCsG+ftansm+cl+ealGl+lPg++++lat++++++l+ ++g+++vel+k+
  lcl|FitnessBrowser__psRCH2:GFF233 168 IAADESASDEKVAEYERSACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHSDREQLFLRAGRTVVELCKR 243
                                        **************************************************************************** PP

                          TIGR00110 230 nik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv 298
                                        ++        Pr+i++++afena+tld+a+GGstnt+Lhlla+a+ea+v+++l  +d lsrkvP+l+k++P+ +k+
  lcl|FitnessBrowser__psRCH2:GFF233 244 YYGegdesvlPRNIASRRAFENAMTLDIAMGGSTNTILHLLAAAQEAEVDFDLRAIDALSRKVPQLCKVAPNIQKY 319
                                        **99999******************************************************************999 PP

                          TIGR00110 299 .iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............................. 344
                                         +ed+hraGG+ ++l+el + gllh+d+ tv  +tlae +++ ++++                             
  lcl|FitnessBrowser__psRCH2:GFF233 320 hMEDVHRAGGIFSILGELARGGLLHTDVPTVHSRTLAEGIAQWDITQtqdeavhtffkagpagiptqtafsqstrw 395
                                        9********************************************999**************************** PP

                          TIGR00110 345 ......vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               ++ +irs+++++++egglavL+Gn+a +G+vvk+agv+e+i +feG+ak++es++ a+++il+ +vk+G
  lcl|FitnessBrowser__psRCH2:GFF233 396 dsldddRENGCIRSVEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIYESQDSAVKGILADEVKAG 471
                                        **77555555****************************************************************** PP

                          TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkiki 490
                                        d+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv+dGDk+ i
  lcl|FitnessBrowser__psRCH2:GFF233 472 DIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDGDKVLI 547
                                        **************************************************************************** PP

                          TIGR00110 491 Dienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542
                                        Di+nr ++l+vs+eel +rr +++kk++       r+v  aL++ya l++sadkGav++
  lcl|FitnessBrowser__psRCH2:GFF233 548 DIPNRSIQLQVSDEELSHRRIEQDKKGWkpaqprtRKVTTALKAYALLATSADKGAVRN 606
                                        ***************************999***9999********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (612 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: 7.86
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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