Alignments for a candidate for ilvD in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Chlorobaculum tepidum TLS

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate NP_661519.1 CT0619 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000006985.1:NP_661519.1
          Length = 560

 Score =  577 bits (1488), Expect = e-169
 Identities = 295/558 (52%), Positives = 397/558 (71%), Gaps = 10/558 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGL--TDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVK 58
           M+SDTIK+G ++APHRSLL   G   T DDF KPFIGI NS+ +++PGH HL+EL    K
Sbjct: 1   MRSDTIKKGFEKAPHRSLLKATGCVSTRDDFSKPFIGICNSFNELIPGHAHLQELGRIAK 60

Query: 59  EGVNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPT 118
           E V  AGGV FEFNT+ +CDGIAM H GM+YSLASRE++AD+VE++  AH LDGLV +P 
Sbjct: 61  EAVREAGGVPFEFNTIGVCDGIAMGHVGMRYSLASRELIADSVETVVEAHRLDGLVCIPN 120

Query: 119 CDKIVPGMLMAAARLDIPAIVVTGGPMLPGEF-KGRKVDLINVYEGVGTVSAGEMSEDEL 177
           CDKI PGM+M A R ++P + V+GGPM  G    G+ VDLI+V+E VG  S GE++EDEL
Sbjct: 121 CDKITPGMMMGALRTNVPVVFVSGGPMKAGHTPSGKTVDLISVFEAVGKCSTGEITEDEL 180

Query: 178 EELERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVE 237
           + +E C CPG  SC+G+FTAN+M CL EALG +LPG  T  A   R+ ++ + +  RI++
Sbjct: 181 QTVEECGCPGCGSCSGMFTANSMNCLCEALGFALPGNGTILAADPRRNELVKAAAGRIID 240

Query: 238 MVQENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRV 297
           +V++ ++P  I+++ +  NA  +DLA+GGSTNT LH  AIA+E + L+ +    ++LS  
Sbjct: 241 LVKKEVRPRQILTRTSMLNAFALDLAMGGSTNTILHTLAIASEAE-LDFDFSELNDLSAK 299

Query: 298 IPHIASISPAGEHMML-DLDRAGGIPAVLKTL---EDHINRECVTCTGRTVQENIENVKV 353
            P+I  +SPA   + + D+DRAGGI A+LK L   E  ++    T TG+T+ ENI + +V
Sbjct: 300 TPYICKVSPATTEVHIEDVDRAGGISAILKELSKVEGLLDLSAPTVTGKTLGENIASAEV 359

Query: 354 GHRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECME 413
             R VIR ++ P  + GGLA+L GNLAP G+VVK GAV+  MM H GPAKV++ +D+ + 
Sbjct: 360 LDRTVIRSVEEPYSTTGGLAVLYGNLAPNGAVVKTGAVSPAMMKHTGPAKVYDCQDDAIA 419

Query: 414 AIFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGP 472
            I  G +  GDV+VIRYEGP+GGPGM EML+PTSAI G GL + VALITDGRFSGG+RG 
Sbjct: 420 GIMNGDVKSGDVVVIRYEGPRGGPGMPEMLSPTSAIIGRGLGDSVALITDGRFSGGSRGA 479

Query: 473 CVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGW 531
           CVGHVSPEA + GP+AAV  GD+I IDIP+R + V L    I +R+++  K    + KG+
Sbjct: 480 CVGHVSPEAADRGPIAAVQTGDMITIDIPARSMTVALDDETIRQRIEALPKFEPKIKKGY 539

Query: 532 LARYRKLAGSADTGAVLR 549
           LARY ++  SA+TGAVL+
Sbjct: 540 LARYARMVTSANTGAVLK 557


Lambda     K      H
   0.319    0.136    0.397 

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: 987
Number of extensions: 50
Number of successful extensions: 8
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: 549
Length of database: 560
Length adjustment: 36
Effective length of query: 513
Effective length of database: 524
Effective search space:   268812
Effective search space used:   268812
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate NP_661519.1 CT0619 (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.24879.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.2e-246  805.4   5.3   1.3e-246  805.2   5.3    1.0  1  lcl|NCBI__GCF_000006985.1:NP_661519.1  CT0619 dihydroxy-acid dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_661519.1  CT0619 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  805.2   5.3  1.3e-246  1.3e-246       1     542 [.      14     557 ..      14     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 805.2 bits;  conditional E-value: 1.3e-246
                              TIGR00110   1 aarallkatGl..kdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                            ++r+llkatG   + +d++kP+i+++ns++e++Pgh hl++l++++ke++++aGgv++efnti+v+DGiamg
  lcl|NCBI__GCF_000006985.1:NP_661519.1  14 PHRSLLKATGCvsTRDDFSKPFIGICNSFNELIPGHAHLQELGRIAKEAVREAGGVPFEFNTIGVCDGIAMG 85 
                                            69********744789******************************************************** PP

                              TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsek 142
                                            h Gm+ysL+sre+iaDsvetvv+ah+lD+lv+i++CDki+PGm+m+alr+n+P+++vsGGpm+ag+t  ++ 
  lcl|NCBI__GCF_000006985.1:NP_661519.1  86 HVGMRYSLASRELIADSVETVVEAHRLDGLVCIPNCDKITPGMMMGALRTNVPVVFVSGGPMKAGHTPSGKT 157
                                            ************************************************************************ PP

                              TIGR00110 143 idlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekke 214
                                            +dl++vfeavg+++ g+++e+el+++e+++cP++gsCsG+ftansm+cl ealG++lPg++t+la++ +++e
  lcl|NCBI__GCF_000006985.1:NP_661519.1 158 VDLISVFEAVGKCSTGEITEDELQTVEECGCPGCGSCSGMFTANSMNCLCEALGFALPGNGTILAADPRRNE 229
                                            ************************************************************************ PP

                              TIGR00110 215 lakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286
                                            l+k ++ ri++lvkk+++Pr+ilt++++ na++ldla+GGstnt+Lh+laia+ea++++++++++ ls k+P
  lcl|NCBI__GCF_000006985.1:NP_661519.1 230 LVKAAAGRIIDLVKKEVRPRQILTRTSMLNAFALDLAMGGSTNTILHTLAIASEAELDFDFSELNDLSAKTP 301
                                            ************************************************************************ PP

                              TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlekvkvlrvdqdvirsldnp 356
                                             ++k++P++ +v ied++raGG+sa+lkel+k egll+  a tvtGktl+e++++++vl  d+ virs+++p
  lcl|NCBI__GCF_000006985.1:NP_661519.1 302 YICKVSPATTEVhIEDVDRAGGISAILKELSKvEGLLDLSAPTVTGKTLGENIASAEVL--DRTVIRSVEEP 371
                                            *********9999*****************99899***********************9..*********** PP

                              TIGR00110 357 vkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgP 428
                                            ++ +gglavL+Gnla++Gavvk+++v+  ++k++Gpakv++ +++a+++i++g+vk GdvvviryeGP+GgP
  lcl|NCBI__GCF_000006985.1:NP_661519.1 372 YSTTGGLAVLYGNLAPNGAVVKTGAVSPAMMKHTGPAKVYDCQDDAIAGIMNGDVKSGDVVVIRYEGPRGGP 443
                                            ************************************************************************ PP

                              TIGR00110 429 GmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldle 500
                                            Gm+emL Ptsa++g GLg++vaLitDGrfsGg+rG ++GhvsPeaa  G+ia v+ GD+i+iDi++r + ++
  lcl|NCBI__GCF_000006985.1:NP_661519.1 444 GMPEMLSPTSAIIGRGLGDSVALITDGRFSGGSRGACVGHVSPEAADRGPIAAVQTGDMITIDIPARSMTVA 515
                                            ************************************************************************ PP

                              TIGR00110 501 vseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                            +++e +++r ++  k e++ +kg+La+ya++v+sa++Gavl+
  lcl|NCBI__GCF_000006985.1:NP_661519.1 516 LDDETIRQRIEALPKFEPKIKKGYLARYARMVTSANTGAVLK 557
                                            ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (560 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: 8.44
//
[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