Alignments for a candidate for ilvD in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfitobacterium hafniense DCB-2

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_011461126.1 DHAF_RS09795 dihydroxy-acid dehydratase

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



>NCBI__GCF_000021925.1:WP_011461126.1
          Length = 556

 Score =  437 bits (1123), Expect = e-127
 Identities = 251/552 (45%), Positives = 346/552 (62%), Gaps = 9/552 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           + S  +  GI+ A  R++    G T +D  KP IG+ +S+++I PG    +ELA+ VK G
Sbjct: 9   VNSQELFEGIKGAYPRAMFKSVGYTQEDLRKPVIGVVSSWSEIHPGSYPNKELAQFVKAG 68

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V AAGG   EF+T+A+CD IA    GM YSL SREIVA  +E M  +   DGLV LP+CD
Sbjct: 69  VWAAGGTPVEFHTIAVCDAIAQGM-GMHYSLPSREIVAAEIELMVGSGGFDGLVFLPSCD 127

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPG-EFKGRKVDLINVYEGVGTVSAGEMSEDELEE 179
           K   GMLMAAARL++PAI +  GPML   + +G++  + ++ EG+G      + E     
Sbjct: 128 KSPAGMLMAAARLNLPAIFLPPGPMLSHFDEQGQQRVMSDIKEGMGAFKKQLIDEKLFAA 187

Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239
           +E   C     C  + T NTM CL EALGMSLPG +T  AV + KR+ A+ +G+RI+ MV
Sbjct: 188 IETDTCTTVGVCGMMGTGNTMGCLIEALGMSLPGTSTTPAVYAEKRRQAKETGQRIMAMV 247

Query: 240 QENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIP 299
           +E+L+P  I++ E+  NAV   +A+GGSTNT LH+PAIA E  G+ + LD  D LS   P
Sbjct: 248 KEDLRPHRILTAESLANAVRFVMAIGGSTNTVLHLPAIAREA-GVELTLDDIDRLSEQTP 306

Query: 300 HIASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVI 359
            IA   P+ ++ + D  +AGG+ AVLK +   +N+E +T TG T++ +   VK  + + +
Sbjct: 307 CIAKYKPSSKYTLWDFYQAGGVGAVLKIMAPLLNQEALTVTGGTIEGHFCEVK--NWETL 364

Query: 360 RPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGR 419
           RPL  P+  +GG+ +L+G+LAP G+V+K   V        G AK F SE+  +E I    
Sbjct: 365 RPLHDPLQPKGGIVVLKGSLAPDGAVIKVSGVKGGPKRQVGTAKTFESEEHLLEHIMTKE 424

Query: 420 IDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHVS 478
           I  GDV+VIR EGP GGPGMREM  P + + GMGL + VA+ITDGRFSG TRG C+GHV+
Sbjct: 425 IQPGDVLVIRNEGPAGGPGMREMSIPAALLTGMGLGDSVAMITDGRFSGATRGFCIGHVA 484

Query: 479 PEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV--KGWLARYR 536
           PEA   GP+A V DGD I IDI  + L + LSP E+ +R+ + + PR+S   KG+L  Y 
Sbjct: 485 PEAHAGGPIAIVRDGDQIEIDIEHKSLNLLLSPGEMTKRM-AELAPRQSPINKGFLGVYA 543

Query: 537 KLAGSADTGAVL 548
           +    AD GAVL
Sbjct: 544 RNVSQADKGAVL 555


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: 900
Number of extensions: 50
Number of successful extensions: 7
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: 556
Length adjustment: 36
Effective length of query: 513
Effective length of database: 520
Effective search space:   266760
Effective search space used:   266760
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_011461126.1 DHAF_RS09795 (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.24869.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-193  629.5   0.5   2.6e-193  629.3   0.5    1.0  1  lcl|NCBI__GCF_000021925.1:WP_011461126.1  DHAF_RS09795 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_011461126.1  DHAF_RS09795 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.3   0.5  2.6e-193  2.6e-193       3     541 ..      24     555 ..      22     556 .] 0.99

  Alignments for each domain:
  == domain 1  score: 629.3 bits;  conditional E-value: 2.6e-193
                                 TIGR00110   3 rallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgh 71 
                                               ra++k++G+++edl kP+i+vv+s++ei Pg    k+la+ vk+++ aaGg+++ef tiav+D ia g 
  lcl|NCBI__GCF_000021925.1:WP_011461126.1  24 RAMFKSVGYTQEDLRKPVIGVVSSWSEIHPGSYPNKELAQFVKAGVWAAGGTPVEFHTIAVCDAIAQG- 91 
                                               8*****************************************************************99. PP

                                 TIGR00110  72 eGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkls 140
                                                Gm+ysLpsrei+a  +e +v +  +D+lv ++sCDk   Gmlmaa+rln+Pai+   Gpm +   + +
  lcl|NCBI__GCF_000021925.1:WP_011461126.1  92 MGMHYSLPSREIVAAEIELMVGSGGFDGLVFLPSCDKSPAGMLMAAARLNLPAIFLPPGPMLSHFDEQG 160
                                               59**************************************************************9999* PP

                                 TIGR00110 141 ekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllats 209
                                               ++  ++d+ e++g+ +++ ++e+   +ie  +c t g C+ + t n+m cl ealG+slPg+st++a+ 
  lcl|NCBI__GCF_000021925.1:WP_011461126.1 161 QQRVMSDIKEGMGAFKKQLIDEKLFAAIETDTCTTVGVCGMMGTGNTMGCLIEALGMSLPGTSTTPAVY 229
                                               ********************************************************************* PP

                                 TIGR00110 210 aekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddf 278
                                               aek++ ak++g+ri+ +vk++++P++ilt e++ na+ +++a+GGstntvLhl+aia+eagv+l+ldd+
  lcl|NCBI__GCF_000021925.1:WP_011461126.1 230 AEKRRQAKETGQRIMAMVKEDLRPHRILTAESLANAVRFVMAIGGSTNTVLHLPAIAREAGVELTLDDI 298
                                               ********************************************************************* PP

                                 TIGR00110 279 drlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdq 347
                                               drls+++P++ak kPs+k+ + d  +aGGv avlk +  + ll+++altvtG t++ +  +vk      
  lcl|NCBI__GCF_000021925.1:WP_011461126.1 299 DRLSEQTPCIAKYKPSSKYTLWDFYQAGGVGAVLKIM--APLLNQEALTVTGGTIEGHFCEVKNW---- 361
                                               *************************************..9****************999988877.... PP

                                 TIGR00110 348 dvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdv 416
                                               + +r+l++p++ +gg+ vLkG+la++Gav+k++gv+    +  G+ak fesee+ le i++++++ Gdv
  lcl|NCBI__GCF_000021925.1:WP_011461126.1 362 ETLRPLHDPLQPKGGIVVLKGSLAPDGAVIKVSGVKGGPKRQVGTAKTFESEEHLLEHIMTKEIQPGDV 430
                                               99******************************************************************* PP

                                 TIGR00110 417 vviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedG 485
                                               +vir eGP GgPGmrem  P++ l+g+GLg++va+itDGrfsG+trG++iGhv+Pea +gG+ia+v+dG
  lcl|NCBI__GCF_000021925.1:WP_011461126.1 431 LVIRNEGPAGGPGMREMSIPAALLTGMGLGDSVAMITDGRFSGATRGFCIGHVAPEAHAGGPIAIVRDG 499
                                               ********************************************************************* PP

                                 TIGR00110 486 DkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               D+i+iDie++ l+l +s  e+ +r a+  +++    kg+L  ya+ vs+adkGavl
  lcl|NCBI__GCF_000021925.1:WP_011461126.1 500 DQIEIDIEHKSLNLLLSPGEMTKRMAELAPRQSPINKGFLGVYARNVSQADKGAVL 555
                                               *******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (556 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: 10.35
//
[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