Alignments for a candidate for ilvD in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Chlorobium phaeobacteroides BS1

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_041471617.1 CPHAMN1_RS08555 dihydroxy-acid dehydratase

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



>NCBI__GCF_000020545.1:WP_041471617.1
          Length = 567

 Score =  563 bits (1450), Expect = e-165
 Identities = 294/558 (52%), Positives = 398/558 (71%), Gaps = 10/558 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGL--TDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVK 58
           M+SDTIK+G ++APHRSLL   G   +++DF KPFIGI NS+ +++PGH HL++L +  K
Sbjct: 1   MRSDTIKKGFEKAPHRSLLKATGALSSNEDFNKPFIGICNSFIELIPGHAHLQKLGQIAK 60

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

Query: 119 CDKIVPGMLMAAARLDIPAIVVTGGPMLPGEF-KGRKVDLINVYEGVGTVSAGEMSEDEL 177
           CDKI PGM+MAA R++IP I V+GGPM  G    G  VDLI+V+E VG  S G +SE+EL
Sbjct: 121 CDKITPGMMMAAVRMNIPVIFVSGGPMKKGRTPSGETVDLISVFEAVGRHSTGAISEEEL 180

Query: 178 EELERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVE 237
             +E  ACP   SC+G+FTAN+M CL EALG +LPG  T  AV  R+ ++ R + +RI++
Sbjct: 181 GVIEDHACPTCGSCSGMFTANSMNCLCEALGFALPGNGTIPAVDPRRLELVREASRRIID 240

Query: 238 MVQENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRV 297
           +V+++ KP  I+S+E+  NA  +D A+GGSTNT LH  A+A E + +  +    ++LS  
Sbjct: 241 LVEKDTKPRDILSRESLLNAFALDFAMGGSTNTILHTLAVANEGE-VVFDFSELNDLSAK 299

Query: 298 IPHIASISPAGEHMML-DLDRAGGIPAVLKTL---EDHINRECVTCTGRTVQENIENVKV 353
            P+I  +SPA +++ + D+DRAGG+ A+LK L   +  ++    T TG+T+ ENIE   +
Sbjct: 300 TPYICKVSPATQNVHIEDVDRAGGVSAILKELSRIDGLLDLTRPTVTGKTLGENIEQAII 359

Query: 354 GHRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECME 413
               VIR + SP  + GGLA+L GNLAP G+VVK GAV+E MM H GPAKV+  +D+ + 
Sbjct: 360 TDSSVIRTVASPYATTGGLAVLYGNLAPEGAVVKTGAVSESMMNHTGPAKVYECQDDALT 419

Query: 414 AIFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGP 472
            I  G +  GDV+VIRYEGPKGGPGM EML+PTSAI G GL E VAL+TDGRFSGG+RG 
Sbjct: 420 GIMEGDVVAGDVVVIRYEGPKGGPGMPEMLSPTSAIMGRGLGESVALLTDGRFSGGSRGA 479

Query: 473 CVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVK-PRRSVKGW 531
           CVGHVSPEA E GP+AAV +GD+I IDIP+R + VDL    I+ERL    +   +   G+
Sbjct: 480 CVGHVSPEAAERGPIAAVRNGDMITIDIPNRTMSVDLPDAAIKERLAQVPQFVPKITTGY 539

Query: 532 LARYRKLAGSADTGAVLR 549
           L+RY ++  SA+TGA+L+
Sbjct: 540 LSRYAQMVTSANTGAILQ 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: 981
Number of extensions: 50
Number of successful extensions: 9
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: 567
Length adjustment: 36
Effective length of query: 513
Effective length of database: 531
Effective search space:   272403
Effective search space used:   272403
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_041471617.1 CPHAMN1_RS08555 (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.13759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.5e-245  799.5   4.0   8.5e-245  799.3   4.0    1.0  1  lcl|NCBI__GCF_000020545.1:WP_041471617.1  CPHAMN1_RS08555 dihydroxy-acid d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_041471617.1  CPHAMN1_RS08555 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  799.3   4.0  8.5e-245  8.5e-245       1     542 [.      14     557 ..      14     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 799.3 bits;  conditional E-value: 8.5e-245
                                 TIGR00110   1 aarallkatGl..kdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGi 67 
                                               ++r+llkatG   ++ed++kP+i+++ns++e++Pgh hl++l++++k+ei++aGgv++efnti+v+DGi
  lcl|NCBI__GCF_000020545.1:WP_041471617.1  14 PHRSLLKATGAlsSNEDFNKPFIGICNSFIELIPGHAHLQKLGQIAKDEIRKAGGVPFEFNTIGVCDGI 82 
                                               69********744789***************************************************** PP

                                 TIGR00110  68 amgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagk 136
                                               amgh Gm+ysL+sre+iaDsvetv++ah+lD+lv+i++CDki+PGm+maa+r+niP+i+vsGGpm++g+
  lcl|NCBI__GCF_000020545.1:WP_041471617.1  83 AMGHLGMRYSLASRELIADSVETVAQAHRLDGLVCIPNCDKITPGMMMAAVRMNIPVIFVSGGPMKKGR 151
                                               ********************************************************************* PP

                                 TIGR00110 137 tklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstl 205
                                               t  +e +dl++vfeavg+ + g +seeel  ie++acPt+gsCsG+ftansm+cl ealG++lPg++t+
  lcl|NCBI__GCF_000020545.1:WP_041471617.1 152 TPSGETVDLISVFEAVGRHSTGAISEEELGVIEDHACPTCGSCSGMFTANSMNCLCEALGFALPGNGTI 220
                                               ********************************************************************* PP

                                 TIGR00110 206 latsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkls 274
                                               +a++ +++el++++++ri++lv+k+ kPrdil++e++ na++ld+a+GGstnt+Lh+la+a+e +v ++
  lcl|NCBI__GCF_000020545.1:WP_041471617.1 221 PAVDPRRLELVREASRRIIDLVEKDTKPRDILSRESLLNAFALDFAMGGSTNTILHTLAVANEGEVVFD 289
                                               ********************************************************************* PP

                                 TIGR00110 275 lddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlekvk 341
                                               +++++ ls k+P ++k++P++++v ied++raGGvsa+lkel++ +gll+    tvtGktl+e++e++ 
  lcl|NCBI__GCF_000020545.1:WP_041471617.1 290 FSELNDLSAKTPYICKVSPATQNVhIEDVDRAGGVSAILKELSRiDGLLDLTRPTVTGKTLGENIEQAI 358
                                               ***********************99******************9889999999**************99 PP

                                 TIGR00110 342 vlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggk 410
                                               ++  d++vir++ +p+  +gglavL+Gnla+eGavvk+++v+e++++++Gpakv+e +++al +i++g+
  lcl|NCBI__GCF_000020545.1:WP_041471617.1 359 IT--DSSVIRTVASPYATTGGLAVLYGNLAPEGAVVKTGAVSESMMNHTGPAKVYECQDDALTGIMEGD 425
                                               99..***************************************************************** PP

                                 TIGR00110 411 vkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGai 479
                                               v +GdvvviryeGPkGgPGm+emL Ptsa++g GLg++vaL+tDGrfsGg+rG ++GhvsPeaae G+i
  lcl|NCBI__GCF_000020545.1:WP_041471617.1 426 VVAGDVVVIRYEGPKGGPGMPEMLSPTSAIMGRGLGESVALLTDGRFSGGSRGACVGHVSPEAAERGPI 494
                                               ********************************************************************* PP

                                 TIGR00110 480 alvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               a v++GD+i+iDi+nr++ +++ ++ ++er a+  +  ++ + g+L++ya++v+sa++Ga+l+
  lcl|NCBI__GCF_000020545.1:WP_041471617.1 495 AAVRNGDMITIDIPNRTMSVDLPDAAIKERLAQVPQFVPKITTGYLSRYAQMVTSANTGAILQ 557
                                               ************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (567 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: 8.70
//
[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