Alignments for a candidate for ilvD in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Chlorobaculum parvum NCIB 8327

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_012501888.1 CPAR_RS03245 dihydroxy-acid dehydratase

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



>NCBI__GCF_000020505.1:WP_012501888.1
          Length = 560

 Score =  578 bits (1491), Expect = e-169
 Identities = 297/557 (53%), Positives = 395/557 (70%), Gaps = 10/557 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGL--TDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVK 58
           M+SDTIK+G ++APHRSLL   G   T DD+ KPFIGI NS+ +++PGH HL+EL    K
Sbjct: 1   MRSDTIKKGFEKAPHRSLLKATGAISTRDDYSKPFIGICNSFNELIPGHAHLQELGRIAK 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 I V+GGPM  G    G+ VDLI+V+E VG  S GE++EDEL
Sbjct: 121 CDKITPGMMMGALRTNVPVIFVSGGPMSAGHTPSGKTVDLISVFEAVGQCSTGEITEDEL 180

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

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

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

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

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

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

Query: 532 LARYRKLAGSADTGAVL 548
           LARY ++  SA+TGAVL
Sbjct: 540 LARYARMVTSANTGAVL 556


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: 995
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 WP_012501888.1 CPAR_RS03245 (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.18307.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-246  804.7   5.1   2.2e-246  804.5   5.1    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012501888.1  CPAR_RS03245 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012501888.1  CPAR_RS03245 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  804.5   5.1  2.2e-246  2.2e-246       1     542 [.      14     557 ..      14     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 804.5 bits;  conditional E-value: 2.2e-246
                                 TIGR00110   1 aarallkatGl..kdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGi 67 
                                               ++r+llkatG   + +d++kP+i+++ns++e++Pgh hl++l++++ke++++aGgv++efnti+v+DGi
  lcl|NCBI__GCF_000020505.1:WP_012501888.1  14 PHRSLLKATGAisTRDDYSKPFIGICNSFNELIPGHAHLQELGRIAKEAVREAGGVPFEFNTIGVCDGI 82 
                                               69********644789***************************************************** PP

                                 TIGR00110  68 amgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagk 136
                                               amgh Gm+ysL+sre+iaDsvetvv+ah+lD+lv+i++CDki+PGm+m+alr+n+P+i+vsGGpm+ag+
  lcl|NCBI__GCF_000020505.1:WP_012501888.1  83 AMGHVGMRYSLASRELIADSVETVVEAHRLDGLVCIPNCDKITPGMMMGALRTNVPVIFVSGGPMSAGH 151
                                               ********************************************************************* PP

                                 TIGR00110 137 tklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstl 205
                                               t  ++ +dl++vfeavg+++ g+++e+el++ie+++cP++gsCsG+ftansm+cl ealG++lPg++t+
  lcl|NCBI__GCF_000020505.1:WP_012501888.1 152 TPSGKTVDLISVFEAVGQCSTGEITEDELQTIEECGCPGCGSCSGMFTANSMNCLCEALGFALPGNGTI 220
                                               ********************************************************************* PP

                                 TIGR00110 206 latsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkls 274
                                               la++ +++el+k ++ riv+lv+k+++Pr+il+++++ na++ldla+GGstnt+Lh+laia+ea+++++
  lcl|NCBI__GCF_000020505.1:WP_012501888.1 221 LAADPRRNELVKAAAGRIVDLVNKDVRPRSILSRQSMLNAFALDLAMGGSTNTILHTLAIASEAELEFD 289
                                               ********************************************************************* PP

                                 TIGR00110 275 lddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlekvk 341
                                               +++++ ls k+P ++k++P++ +v ied++raGG+sa+lkel+k egll+  a tvtGktl+e++++++
  lcl|NCBI__GCF_000020505.1:WP_012501888.1 290 FSELNDLSAKTPYICKVSPATTEVhIEDVDRAGGISAILKELSKvEGLLDLSAPTVTGKTLGENIADAE 358
                                               *********************9999*****************99899********************** PP

                                 TIGR00110 342 vlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggk 410
                                               vl  d++virs+++p++++gglavL+Gnla++G+vvk+++v+ +++k++Gpakv++ +++a+++i++g+
  lcl|NCBI__GCF_000020505.1:WP_012501888.1 359 VL--DRSVIRSVEEPYSATGGLAVLYGNLAPNGSVVKTGAVSPSMMKHTGPAKVYDCQDDAIAGIMNGD 425
                                               *9..***************************************************************** PP

                                 TIGR00110 411 vkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGai 479
                                               vk GdvvviryeGP+GgPGm+emL Ptsa++g GLg++vaLitDGrfsGg+rG ++GhvsPeaa  G+i
  lcl|NCBI__GCF_000020505.1:WP_012501888.1 426 VKSGDVVVIRYEGPRGGPGMPEMLSPTSAIMGRGLGDSVALITDGRFSGGSRGACVGHVSPEAADRGPI 494
                                               ********************************************************************* PP

                                 TIGR00110 480 alvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               a v+ GD+i+iDi+ r++ +++++e +++r ++  + e++ +kg+La+ya++v+sa++Gavl+
  lcl|NCBI__GCF_000020505.1:WP_012501888.1 495 AAVQTGDMITIDIPGRTMSVALDDETIRQRIEALPEFEPKIKKGYLARYARMVTSANTGAVLT 557
                                               *************************************************************85 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: 00:00:00.02
# Mc/sec: 11.58
//
[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