Alignments for a candidate for ilvD in Thioalkalivibrio halophilus HL17

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Thioalkalivibrio halophilus HL17

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_077243522.1 B1A74_RS01110 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_001995255.1:WP_077243522.1
          Length = 561

 Score =  720 bits (1859), Expect = 0.0
 Identities = 360/555 (64%), Positives = 437/555 (78%), Gaps = 1/555 (0%)

Query: 4   NKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAID 63
           N+RS+ +T+G  R+PNR+M  A+G+  +DF +P+VGIAN HSTITPCN G+  LA+ A  
Sbjct: 5   NRRSRVVTEGPRRTPNRAMLRAVGFGDDDFQRPIVGIANAHSTITPCNTGIGALAERAER 64

Query: 64  AIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGC 123
           A++ +   PQ FGT TISDG+SMGT GMKYSL+SREVIAD IET   GQ MDGV+  GGC
Sbjct: 65  AVRQAGGMPQTFGTITISDGISMGTPGMKYSLVSREVIADAIETVVNGQSMDGVLATGGC 124

Query: 124 DKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEG 183
           DKNMPG MIALAR NVPGI+VYGGTIKPG++KG++LTIVS+FEAVG+  AGR+S ED +G
Sbjct: 125 DKNMPGAMIALARLNVPGIFVYGGTIKPGHYKGQELTIVSAFEAVGQHGAGRLSDEDLQG 184

Query: 184 VEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAI 243
           VE+NACP  GSCGGMYTANTMSS+FEALGMSL  SST A  D EK +SAA S  VL+EAI
Sbjct: 185 VERNACPGAGSCGGMYTANTMSSAFEALGMSLPGSSTQAAEDPEKGESAARSGEVLLEAI 244

Query: 244 KQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPV 303
             D KPRDI+TR + ENA+A++MA GGSTNAVLH LAIAHAAEV   +DD ERIRR+ PV
Sbjct: 245 HADRKPRDILTRPAFENALAVVMALGGSTNAVLHLLAIAHAAEVPLDLDDVERIRRRTPV 304

Query: 304 ICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRAD 363
           +C+LKPSG+YV T  H+AGG P VM++LL AG+LHG+CLTITG TLAE L + P  P A+
Sbjct: 305 LCDLKPSGRYVTTAFHQAGGTPLVMRLLLDAGLLHGECLTITGETLAETLRDAPAAPPAE 364

Query: 364 -QDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAIL 422
             D++      LY +GHLAILKG+LA EG VAK+TGLK   I GPARVF+ E+  ++AIL
Sbjct: 365 ATDMVRTPADPLYPQGHLAILKGSLAPEGGVAKVTGLKRRSIRGPARVFDSEEDCLDAIL 424

Query: 423 ADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVG 482
           A KI  GD++V+R+ GP+GGPGM EMLAPT+A+IG GLG++VG +TDGRFSGGT+GMVVG
Sbjct: 425 AGKIREGDVIVIRHEGPRGGPGMREMLAPTAALIGAGLGDAVGLVTDGRFSGGTYGMVVG 484

Query: 483 HVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAK 542
           HVAPEA  GG IALVQEGD I IDA +  L L++  EEL RRRA WK P P   RGVLAK
Sbjct: 485 HVAPEAAAGGPIALVQEGDPIVIDADRNQLDLDIDPEELERRRAAWKAPEPPVARGVLAK 544

Query: 543 FSKLASTASKGAVTD 557
           +++   +AS+GAVTD
Sbjct: 545 YARTVGSASRGAVTD 559


Lambda     K      H
   0.316    0.133    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: 1062
Number of extensions: 51
Number of successful extensions: 2
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: 557
Length of database: 561
Length adjustment: 36
Effective length of query: 521
Effective length of database: 525
Effective search space:   273525
Effective search space used:   273525
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_077243522.1 B1A74_RS01110 (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.680525.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-231  754.8   1.1   2.9e-231  754.6   1.1    1.0  1  NCBI__GCF_001995255.1:WP_077243522.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001995255.1:WP_077243522.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  754.6   1.1  2.9e-231  2.9e-231       1     542 [.      19     559 ..      19     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: 754.6 bits;  conditional E-value: 2.9e-231
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++ra+l+a+G+ d+d+++Pi++++n++++i+P++  +  la+++++++++aGg+++ f+ti++sDGi+mg+ G
  NCBI__GCF_001995255.1:WP_077243522.1  19 PNRAMLRAVGFGDDDFQRPIVGIANAHSTITPCNTGIGALAERAERAVRQAGGMPQTFGTITISDGISMGTPG 91 
                                           68*********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           mkysL+sre+iaD++etvv+++ +D++++ + CDk++PG+++a +rln+P i+v+GG++++g++k ++++++v
  NCBI__GCF_001995255.1:WP_077243522.1  92 MKYSLVSREVIADAIETVVNGQSMDGVLATGGCDKNMPGAMIALARLNVPGIFVYGGTIKPGHYK-GQELTIV 163
                                           *****************************************************************.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           ++feavg+  ag+ls+e+l+ +er+acP+agsC+G++tan+m++++ealG+slPgsst +a + ek e+a +s
  NCBI__GCF_001995255.1:WP_077243522.1 164 SAFEAVGQHGAGRLSDEDLQGVERNACPGAGSCGGMYTANTMSSAFEALGMSLPGSSTQAAEDPEKGESAARS 236
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g+ + e+++ + kPrdilt+ afena+++++alGGstn+vLhllaia+ a+v l+ldd++r++r++P+l++lk
  NCBI__GCF_001995255.1:WP_077243522.1 237 GEVLLEAIHADRKPRDILTRPAFENALAVVMALGGSTNAVLHLLAIAHAAEVPLDLDDVERIRRRTPVLCDLK 309
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr..vdqdvirsldnpvkkeggl 363
                                           Psg++v++  h+aGG++ v++ l  +gllh ++lt+tG+tlaetl +++  +  + +d++r+  +p++ +g+l
  NCBI__GCF_001995255.1:WP_077243522.1 310 PSGRYVTTAFHQAGGTPLVMRLLLDAGLLHGECLTITGETLAETLRDAPAAPpaEATDMVRTPADPLYPQGHL 382
                                           ************************************************9997667889*************** PP

                             TIGR00110 364 avLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaP 436
                                           a+LkG+la+eG v+k++g +     ++Gpa+vf+see++l+ail+gk++eGdv+vir+eGP+GgPGmremLaP
  NCBI__GCF_001995255.1:WP_077243522.1 383 AILKGSLAPEGGVAKVTGLKR--RSIRGPARVFDSEEDCLDAILAGKIREGDVIVIRHEGPRGGPGMREMLAP 453
                                           ********************9..899*********************************************** PP

                             TIGR00110 437 tsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaer 509
                                           t+al+g+GLg++v+L+tDGrfsGgt+G+++Ghv+Peaa+gG+ialv++GD i iD+++++ldl+++ eel++r
  NCBI__GCF_001995255.1:WP_077243522.1 454 TAALIGAGLGDAVGLVTDGRFSGGTYGMVVGHVAPEAAAGGPIALVQEGDPIVIDADRNQLDLDIDPEELERR 526
                                           ************************************************************************* PP

                             TIGR00110 510 rakakkkearevkgaLakyaklvssadkGavld 542
                                           ra++k++e+   +g+Lakya+ v sa++Gav+d
  NCBI__GCF_001995255.1:WP_077243522.1 527 RAAWKAPEPPVARGVLAKYARTVGSASRGAVTD 559
                                           *******************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (561 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.60
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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