Alignments for a candidate for ilvD in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Nocardiopsis lucentensis DSM 44048

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_083924308.1 D471_RS0123680 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>NCBI__GCF_000341125.1:WP_083924308.1
          Length = 620

 Score =  851 bits (2199), Expect = 0.0
 Identities = 426/621 (68%), Positives = 505/621 (81%), Gaps = 6/621 (0%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP  RSRT THGRNMAGAR L RATG++ EDFGKPI+AVANSFT+FVPGHVHL+ +  +V
Sbjct: 1   MPALRSRTVTHGRNMAGARALMRATGVEREDFGKPIVAVANSFTEFVPGHVHLRQVADVV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           A  I  AGGV +EFN+IAVDDGIAMGH GMLYSLPSR+LIADSVEYMVNAHCADA+VC+S
Sbjct: 61  AGAIREAGGVPREFNSIAVDDGIAMGHSGMLYSLPSRELIADSVEYMVNAHCADALVCVS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKG----KIRALDLVDAMVVAADDSY 176
           NCDKITPGML+AA+RLNIP VFVSGGPMEAGKVTV       +R LDL++ M+ +AD+S 
Sbjct: 121 NCDKITPGMLLAALRLNIPTVFVSGGPMEAGKVTVVDGTATTVRKLDLINPMIASADESV 180

Query: 177 SDEEVEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAG 236
           S  E++ +E+AACPTCGSCSGMFTANSMNCLTEA+GL+LPGNG+VLATH  R AL+++AG
Sbjct: 181 SQAELDEMEEAACPTCGSCSGMFTANSMNCLTEAMGLALPGNGTVLATHTARRALYEDAG 240

Query: 237 RVVVDLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDF 296
           R+VV+  +R+YE +DA+ LP  IAT AAF NAM+LD+AMGGSTNT+LHLLAAA E G+DF
Sbjct: 241 RLVVEAAKRYYEDDDASVLPLSIATPAAFGNAMALDVAMGGSTNTILHLLAAATEAGVDF 300

Query: 297 SMADIDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPT 356
            + +ID +SR VPCL KVAP     H+EDVHRAGG+ AILGEL RGGL+D S PTVH  T
Sbjct: 301 GLTEIDAVSRRVPCLCKVAPNTEKYHIEDVHRAGGIPAILGELARGGLLDTSLPTVHGKT 360

Query: 357 MGEALARWDIGR-TNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHP 415
           +GE +A WD+   T S  A E F AAPGG+ T  A+SQ+ RW+ LD DRE G +RSV H 
Sbjct: 361 VGEFIAEWDVATDTVSDEAVELFHAAPGGRRTTKAYSQSTRWDSLDTDREKGCVRSVPHA 420

Query: 416 FSKDGGLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEV 475
           ++KDGGLAVLFGNLAP+G IVKTAGV+E + TF G A+VFESQ+ AV GIL  Q++ G+V
Sbjct: 421 YTKDGGLAVLFGNLAPDGAIVKTAGVEEELWTFSGPAKVFESQEDAVEGILTKQIEPGDV 480

Query: 476 VVIRYEGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEG 535
           VVIRYEGPKGGPGMQEMLYPT++LK +GLG ACAL+TDGRFSGGTSGLSIGH SPEA  G
Sbjct: 481 VVIRYEGPKGGPGMQEMLYPTSFLKGRGLGKACALITDGRFSGGTSGLSIGHASPEAAAG 540

Query: 536 GLIALVETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRA 595
           G IALVE GD I IDIP RGI LEV++  L+ARRE +L +    + P +R+R +T ALRA
Sbjct: 541 GDIALVEDGDVISIDIPNRGIVLEVAEDELSARRE-RLLKELGRFQPRDRQRPVTAALRA 599

Query: 596 YAAMTTNAARGAVRDVSQIER 616
           YAAM T+A+ GA RDVSQIER
Sbjct: 600 YAAMATSASTGAARDVSQIER 620


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: 1266
Number of extensions: 48
Number of successful extensions: 4
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: 620
Length adjustment: 37
Effective length of query: 580
Effective length of database: 583
Effective search space:   338140
Effective search space used:   338140
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 WP_083924308.1 D471_RS0123680 (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.17411.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.1e-241  786.8   1.9   5.9e-241  786.6   1.9    1.0  1  lcl|NCBI__GCF_000341125.1:WP_083924308.1  D471_RS0123680 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_083924308.1  D471_RS0123680 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  786.6   1.9  5.9e-241  5.9e-241       2     542 ..      18     614 ..      17     615 .. 0.97

  Alignments for each domain:
  == domain 1  score: 786.6 bits;  conditional E-value: 5.9e-241
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG++ ed++kPi+av+ns+te+vPghvhl+++a++v+ +i++aGgv+ efn iav+DGiamg
  lcl|NCBI__GCF_000341125.1:WP_083924308.1  18 ARALMRATGVEREDFGKPIVAVANSFTEFVPGHVHLRQVADVVAGAIREAGGVPREFNSIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaDsve++v+ah++Dalv++s+CDki+PGml+aalrlniP+++vsGGpmeagk+++
  lcl|NCBI__GCF_000341125.1:WP_083924308.1  87 HSGMLYSLPSRELIADSVEYMVNAHCADALVCVSNCDKITPGMLLAALRLNIPTVFVSGGPMEAGKVTV 155
                                               *******************************************************************99 PP

                                 TIGR00110 140 ....sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsst 204
                                                   +  + ++d+++ +++ a++ +s++el+e+e+ acPt+gsCsG+ftansm+cltea+Gl+lPg++t
  lcl|NCBI__GCF_000341125.1:WP_083924308.1 156 vdgtATTVRKLDLINPMIASADESVSQAELDEMEEAACPTCGSCSGMFTANSMNCLTEAMGLALPGNGT 224
                                               787778999************************************************************ PP

                                 TIGR00110 205 llatsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaia 266
                                               +lat++ +++l + +g+ +ve+ k++++       P +i+t +af na++ld+a+GGstnt+Lhlla+a
  lcl|NCBI__GCF_000341125.1:WP_083924308.1 225 VLATHTARRALYEDAGRLVVEAAKRYYEdddasvlPLSIATPAAFGNAMALDVAMGGSTNTILHLLAAA 293
                                               ********************************************************************* PP

                                 TIGR00110 267 keagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktla 334
                                                eagv++ l ++d +sr+vP+l+k++P+++k+ ied+hraGG++a+l+el + gll++   tv Gkt++
  lcl|NCBI__GCF_000341125.1:WP_083924308.1 294 TEAGVDFGLTEIDAVSRRVPCLCKVAPNTEKYhIEDVHRAGGIPAILGELARGGLLDTSLPTVHGKTVG 362
                                               *******************************99************************************ PP

                                 TIGR00110 335 etlekvkvlr....................................vdqdvirsldnpvkkegglavLk 367
                                               e +++ +v +                                     ++ ++rs+ ++++k+gglavL+
  lcl|NCBI__GCF_000341125.1:WP_083924308.1 363 EFIAEWDVATdtvsdeavelfhaapggrrttkaysqstrwdsldtdREKGCVRSVPHAYTKDGGLAVLF 431
                                               ********999*******************************88555555******************* PP

                                 TIGR00110 368 GnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaP 436
                                               Gnla++Ga+vk+agvee++++f Gpakvfes+e+a+e+il+++++ GdvvviryeGPkGgPGm+emL+P
  lcl|NCBI__GCF_000341125.1:WP_083924308.1 432 GNLAPDGAIVKTAGVEEELWTFSGPAKVFESQEDAVEGILTKQIEPGDVVVIRYEGPKGGPGMQEMLYP 500
                                               ********************************************************************* PP

                                 TIGR00110 437 tsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseee 505
                                               ts+l+g GLgk++aLitDGrfsGgt+GlsiGh sPeaa+gG ialvedGD i+iDi+nr + lev e+e
  lcl|NCBI__GCF_000341125.1:WP_083924308.1 501 TSFLKGRGLGKACALITDGRFSGGTSGLSIGHASPEAAAGGDIALVEDGDVISIDIPNRGIVLEVAEDE 569
                                               ********************************************************************* PP

                                 TIGR00110 506 laerrakakkkea........revkgaLakyaklvssadkGavld 542
                                               l +rr++  k+          r v  aL++ya +++sa++Ga++d
  lcl|NCBI__GCF_000341125.1:WP_083924308.1 570 LSARRERLLKELGrfqprdrqRPVTAALRAYAAMATSASTGAARD 614
                                               ****998765543567778778999*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (620 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: 00:00:00.02
# Mc/sec: 12.83
//
[ok]

This GapMind analysis is from Apr 10 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