Alignments for a candidate for ilvD in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Dechlorosoma suillum PS

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Dsui_1122 Dsui_1122 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__PS:Dsui_1122
          Length = 619

 Score =  949 bits (2454), Expect = 0.0
 Identities = 468/612 (76%), Positives = 529/612 (86%), Gaps = 3/612 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRSRT+THGRNMAGAR LWRATGMKD DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPAYRSRTSTHGRNMAGARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIEAAGG+AKEFNTIA+DDGIAMGHDGMLYSLPSR+LIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGIAKEFNTIAIDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGMLMA++R+NIPT+FVSGGPMEAGKV   GKT A+DL+DAM+ A D   SD +
Sbjct: 121 NCDKITPGMLMAAMRVNIPTIFVSGGPMEAGKVKWEGKTIAVDLIDAMIKAGDSNCSDAE 180

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           V+  ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH DRK LF+EAG  IV
Sbjct: 181 VEEFERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTLVATHADRKGLFLEAGRRIV 240

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
            LA+R+YE++D   LPR+IA+++AFENA  LD+AMGGSTNTVLH+LA A E  + FTMAD
Sbjct: 241 RLAQRWYEENDASVLPRSIANQKAFENAFALDVAMGGSTNTVLHLLATAQEAGVTFTMAD 300

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           IDA+SR+VPCL KVAPA  D H+EDVHRAGGIM+ILGEL +GGL++RD PTVH  TLG+A
Sbjct: 301 IDAISRKVPCLCKVAPATQDYHIEDVHRAGGIMAILGELSRGGLIHRDTPTVHCHTLGEA 360

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           ID +D+ R  S+   +F+RAAPGGIPTQ AFSQ+ R+ ELD DR NG IR+V H +SK+G
Sbjct: 361 IDTYDVQRAGSQRTLEFFRAAPGGIPTQTAFSQDRRYTELDQDRSNGCIRNVAHAYSKEG 420

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVL GN+A+DGCIVKTAGVDESI KF+G A+V+ESQD++V AIL  EV AGDVVVIRY
Sbjct: 421 GLAVLHGNIALDGCIVKTAGVDESIWKFTGKAKVYESQDSAVTAILGGEVVAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGPKGGPGMQEMLYPTSYLKS+GLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSRGLGKECALLTDGRFSGGTSGLSIGHASPEAAEGGAIGL 540

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597
           VR GD I+IDIP R I L VS+ EL  RRAE++AKG   W PTE R R V+ AL+AYA  
Sbjct: 541 VRTGDTIEIDIPGRRIHLAVSDAELEKRRAEENAKGDKAWKPTEERGRVVSKALQAYALM 600

Query: 598 ATSADRGAVRDL 609
           ATSAD+GAVRDL
Sbjct: 601 ATSADKGAVRDL 612


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: 1329
Number of extensions: 38
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: 619
Length adjustment: 37
Effective length of query: 575
Effective length of database: 582
Effective search space:   334650
Effective search space used:   334650
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 Dsui_1122 Dsui_1122 (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.2391.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-258  844.2   3.2   2.5e-258  844.0   3.2    1.0  1  lcl|FitnessBrowser__PS:Dsui_1122  Dsui_1122 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1122  Dsui_1122 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  844.0   3.2  2.5e-258  2.5e-258       2     542 ..      18     611 ..      17     612 .. 0.99

  Alignments for each domain:
  == domain 1  score: 844.0 bits;  conditional E-value: 2.5e-258
                         TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysL 78 
                                       aral++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGg+akefntia++DGiamgh+Gm+ysL
  lcl|FitnessBrowser__PS:Dsui_1122  18 ARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGIAKEFNTIAIDDGIAMGHDGMLYSL 94 
                                       79*************************************************************************** PP

                         TIGR00110  79 psreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgey 155
                                       psr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+r+niP+i+vsGGpmeagk+k   k + vd+++a++++
  lcl|FitnessBrowser__PS:Dsui_1122  95 PSRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRVNIPTIFVSGGPMEAGKVKWEGKTIAVDLIDAMIKA 171
                                       ***************************************************************************** PP

                         TIGR00110 156 aagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik 232
                                        +++ s++e+ee+ersacPt+gsCsG+ftansm+cltealGlslPg++tl at+a++k l+ ++g+riv l ++ ++
  lcl|FitnessBrowser__PS:Dsui_1122 172 GDSNCSDAEVEEFERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTLVATHADRKGLFLEAGRRIVRLAQRWYE 248
                                       ****************************************************************************9 PP

                         TIGR00110 233 .......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.ied 301
                                              Pr+i++++afena++ld+a+GGstntvLhlla a+eagv++++ d+d +srkvP+l+k++P+++ + ied
  lcl|FitnessBrowser__PS:Dsui_1122 249 endasvlPRSIANQKAFENAFALDVAMGGSTNTVLHLLATAQEAGVTFTMADIDAISRKVPCLCKVAPATQDYhIED 325
                                       9**********************************************************************999*** PP

                         TIGR00110 302 lhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr...............................vdq 347
                                       +hraGG++a+l+el++ gl+h+d+ tv  +tl+e +++++v+r                               +dq
  lcl|FitnessBrowser__PS:Dsui_1122 326 VHRAGGIMAILGELSRGGLIHRDTPTVHCHTLGEAIDTYDVQRagsqrtleffraapggiptqtafsqdrryteLDQ 402
                                       *************************************************************************9455 PP

                         TIGR00110 348 d....virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvvir 420
                                       d    +ir++ ++++kegglavL+Gn+a +G++vk+agv+e+i+kf+G+akv+es++ a+ ailgg+v +Gdvvvir
  lcl|FitnessBrowser__PS:Dsui_1122 403 DrsngCIRNVAHAYSKEGGLAVLHGNIALDGCIVKTAGVDESIWKFTGKAKVYESQDSAVTAILGGEVVAGDVVVIR 479
                                       45567************************************************************************ PP

                         TIGR00110 421 yeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkl 497
                                       yeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaaegGai+lv+ GD+i+iDi+ r++
  lcl|FitnessBrowser__PS:Dsui_1122 480 YEGPKGGPGMQEMLYPTSYLKSRGLGKECALLTDGRFSGGTSGLSIGHASPEAAEGGAIGLVRTGDTIEIDIPGRRI 556
                                       ***************************************************************************** PP

                         TIGR00110 498 dlevseeelaerrakakkkea..........revkgaLakyaklvssadkGavld 542
                                       +l+vs++el++rra+ ++k++          r v+ aL++ya +++sadkGav+d
  lcl|FitnessBrowser__PS:Dsui_1122 557 HLAVSDAELEKRRAEENAKGDkawkpteergRVVSKALQAYALMATSADKGAVRD 611
                                       *******************99999*****************************97 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.63
//
[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