Alignments for a candidate for ilvD in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Thermomonospora curvata DSM 43183

Align dihydroxyacid dehydratase (characterized)
to candidate WP_012851710.1 TCUR_RS06615 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_000024385.1:WP_012851710.1
          Length = 618

 Score =  839 bits (2168), Expect = 0.0
 Identities = 421/620 (67%), Positives = 502/620 (80%), Gaps = 7/620 (1%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP  RS T THGRNMAGARAL RATG+   DFGKPI+AV NSFTQFVPGHVHLR++G++V
Sbjct: 1   MPPLRSRTVTHGRNMAGARALLRATGVAREDFGKPIVAVANSFTQFVPGHVHLREVGEVV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AE +  AGGV +EFNTIAVDDGIAMGH GMLYSLPSRELIAD+VEYMV AH ADA++C+S
Sbjct: 61  AEAVREAGGVPREFNTIAVDDGIAMGHDGMLYSLPSRELIADAVEYMVQAHRADALICLS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLS-DQIIKLDLVDAMIQGADPKVSDS 179
           NCDKITPGML+A+LRLNIP +FVSGGPMEAGK         KLDL+D+MI  AD  VSD 
Sbjct: 121 NCDKITPGMLLAALRLNIPTVFVSGGPMEAGKPVSGVSGGHKLDLIDSMIASADTGVSDE 180

Query: 180 QSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRI 239
              QVE +ACPTCGSCSGMFTANSMNCLTEA+GL+ PGNG++LATHA RK+LF +AG+R+
Sbjct: 181 ALAQVEENACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTILATHAARKKLFADAGRRV 240

Query: 240 VELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMS 299
           VE+ KRYYE +DES LP +IA++ AFENAM LD+AMGGSTNT+LHLLAAA EA +DF + 
Sbjct: 241 VEIAKRYYEDDDESVLPLSIATRDAFENAMALDVAMGGSTNTILHLLAAATEAGVDFGLK 300

Query: 300 DIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQ 359
           DID+LSR+VP +CKVAP+T KYH+EDVHRAGG+  +LGELDRAGL+NRD + V   T+ +
Sbjct: 301 DIDELSRRVPCICKVAPATGKYHIEDVHRAGGIPALLGELDRAGLINRDARTVHAATVGE 360

Query: 360 TLEQYDVMLTQD-DAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSK 418
            + ++DV   +     + ++ A P G+RTTQA+SQ  RWD LD DR +GCIR +EHAY+ 
Sbjct: 361 FIAKWDVRSPEVLPQARELWHAAPGGVRTTQAYSQSSRWDELDLDRESGCIRDIEHAYTA 420

Query: 419 DGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVI 478
           DGGLAVLYGN A +G IVKTAGV++ +  F+GPA V+ESQ++AVE ILGGKV  GDVVVI
Sbjct: 421 DGGLAVLYGNIAPDGAIVKTAGVEEELWTFSGPAVVFESQEEAVEGILGGKVKEGDVVVI 480

Query: 479 RYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSI 538
           RYEGPKGGPGMQEMLYPTSFLK  GLGKACALITDGRFSGGTSGLSIGHVSPEAA+GG+I
Sbjct: 481 RYEGPKGGPGMQEMLYPTSFLKGRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGAI 540

Query: 539 GLIEDGDLIAIDIPNRGIQLQVSDAELAARRE--AQDARGDKAWTPKNRERQVSFALRAY 596
            L+E+GD I IDIP R ++L V + ELAARRE    D  G   + P++R R +S AL+AY
Sbjct: 541 ALVENGDRIVIDIPRRSLELDVPEEELAARREKLLADLGG---YRPRDRHRPISAALQAY 597

Query: 597 ASLATSADKGAVRDKSKLGG 616
           A++ATSA  GA RD  +L G
Sbjct: 598 AAMATSASTGAARDIGQLTG 617


Lambda     K      H
   0.317    0.134    0.386 

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: 1243
Number of extensions: 53
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: 616
Length of database: 618
Length adjustment: 37
Effective length of query: 579
Effective length of database: 581
Effective search space:   336399
Effective search space used:   336399
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_012851710.1 TCUR_RS06615 (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.22103.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-250  816.2   0.6   7.3e-250  816.0   0.6    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012851710.1  TCUR_RS06615 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012851710.1  TCUR_RS06615 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  816.0   0.6  7.3e-250  7.3e-250       2     542 ..      18     611 ..      17     612 .. 0.97

  Alignments for each domain:
  == domain 1  score: 816.0 bits;  conditional E-value: 7.3e-250
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               arall+atG+  ed++kPi+av+ns+t++vPghvhl++++++v+e++++aGgv+ efntiav+DGiamg
  lcl|NCBI__GCF_000024385.1:WP_012851710.1  18 ARALLRATGVAREDFGKPIVAVANSFTQFVPGHVHLREVGEVVAEAVREAGGVPREFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaD+ve++v+ah++Dal+++s+CDki+PGml+aalrlniP+++vsGGpmeagk   
  lcl|NCBI__GCF_000024385.1:WP_012851710.1  87 HDGMLYSLPSRELIADAVEYMVQAHRADALICLSNCDKITPGMLLAALRLNIPTVFVSGGPMEAGKPVS 155
                                               ******************************************************************987 PP

                                 TIGR00110 140 s.ekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                               + +  +++d+++++++ a+  +s+e l ++e++acPt+gsCsG+ftansm+cltea+Gl+lPg++t+la
  lcl|NCBI__GCF_000024385.1:WP_012851710.1 156 GvSGGHKLDLIDSMIASADTGVSDEALAQVEENACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTILA 224
                                               52456899************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakea 269
                                               t+a +k+l+  +g+r+ve+ k++++       P +i+t++afena++ld+a+GGstnt+Lhlla+a ea
  lcl|NCBI__GCF_000024385.1:WP_012851710.1 225 THAARKKLFADAGRRVVEIAKRYYEdddesvlPLSIATRDAFENAMALDVAMGGSTNTILHLLAAATEA 293
                                               ********************************************************************* PP

                                 TIGR00110 270 gvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetl 337
                                               gv++ l+d+d+lsr+vP+++k++P++ k+ ied+hraGG++a+l+eld++gl+++da tv   t++e +
  lcl|NCBI__GCF_000024385.1:WP_012851710.1 294 GVDFGLKDIDELSRRVPCICKVAPATGKYhIEDVHRAGGIPALLGELDRAGLINRDARTVHAATVGEFI 362
                                               *************************98888*************************************** PP

                                 TIGR00110 338 ekvkvlr....................................vdqdvirsldnpvkkegglavLkGnl 370
                                               +k +v+                                      ++ +ir ++++++++gglavL+Gn+
  lcl|NCBI__GCF_000024385.1:WP_012851710.1 363 AKWDVRSpevlpqarelwhaapggvrttqaysqssrwdeldldRESGCIRDIEHAYTADGGLAVLYGNI 431
                                               *****999*******************************88544455********************** PP

                                 TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439
                                               a++Ga+vk+agvee++++f Gpa vfes+eea+e+ilggkvkeGdvvviryeGPkGgPGm+emL+Pts+
  lcl|NCBI__GCF_000024385.1:WP_012851710.1 432 APDGAIVKTAGVEEELWTFSGPAVVFESQEEAVEGILGGKVKEGDVVVIRYEGPKGGPGMQEMLYPTSF 500
                                               ********************************************************************* PP

                                 TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508
                                               l+g GLgk++aLitDGrfsGgt+GlsiGhvsPeaa+gGaialve+GD+i iDi++r l+l+v eeela+
  lcl|NCBI__GCF_000024385.1:WP_012851710.1 501 LKGRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGAIALVENGDRIVIDIPRRSLELDVPEEELAA 569
                                               ********************************************************************* PP

                                 TIGR00110 509 rrakakkkea........revkgaLakyaklvssadkGavld 542
                                               rr+k  +           r ++ aL++ya +++sa++Ga++d
  lcl|NCBI__GCF_000024385.1:WP_012851710.1 570 RREKLLADLGgyrprdrhRPISAALQAYAAMATSASTGAARD 611
                                               ***987655456777778999******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (618 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: 7.92
//
[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