Alignments for a candidate for ilvD in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Rhodospirillum centenum SW SW; ATCC 51521

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_012566366.1 RC1_RS05545 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000016185.1:WP_012566366.1
          Length = 577

 Score =  560 bits (1443), Expect = e-164
 Identities = 291/553 (52%), Positives = 374/553 (67%), Gaps = 6/553 (1%)

Query: 21  SRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVF 80
           SR V+ G E+A  R    A+GM +++ A+P +GVA+ WNE  PCN++L+R A AVK GV 
Sbjct: 16  SRHVSVGPERAPHRSYYYAMGMTEQEIARPFVGVATCWNEAAPCNIALNRQAQAVKTGVK 75

Query: 81  SAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKS 140
           +  G P EF TI+V+DGI+MGH+GM  SLVSREVIADSVE+ M+    D  V LAGCDKS
Sbjct: 76  AEQGTPREFTTITVTDGIAMGHQGMKASLVSREVIADSVELTMRGHCYDALVGLAGCDKS 135

Query: 141 LPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADV 200
           LPGM+MA  RL++ +VF+Y GSILPG+ +      +DVT+ D FEAVGA S G M   D+
Sbjct: 136 LPGMMMAMVRLNVPSVFMYGGSILPGKFR-----GKDVTVQDVFEAVGAFSAGRMDEKDL 190

Query: 201 DAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVE 260
             +E   CPG GACGG YTANTMA  +EA+G++LPGSA  PA    RD +A  SG+AV++
Sbjct: 191 HELECCACPGSGACGGQYTANTMACVSEAIGLALPGSAGAPAPYESRDAYAEASGRAVMK 250

Query: 261 LLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGV 320
           L+   +  RDI+T++A ENA  VV A GGSTNA LHL AIAHEA +   L D + +    
Sbjct: 251 LVEMNLRPRDIVTRKALENAAVVVAASGGSTNAALHLPAIAHEAGIEFDLHDVAAVFRRT 310

Query: 321 PHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPDP 380
           P++AD+KP GR V  D+  +GGVPV+MKALLD G LHGDC+TVTG T+AENLA +  P  
Sbjct: 311 PYIADLKPGGRFVAKDLFEVGGVPVLMKALLDGGFLHGDCITVTGRTIAENLADVVFP-T 369

Query: 381 DGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAALDALE 440
           D +V+R  + P+ P+GG+  L G+LAP+GA+VK AG  +  F G AR FD E  A  A+E
Sbjct: 370 DQEVIRPTSAPLSPTGGVVGLRGNLAPQGAIVKVAGMKNLRFSGPARCFDREEDAFAAVE 429

Query: 441 DGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVG 500
                 G+ +VIRYEGP+GGPGMREMLA T A+ G G+G  V L+TDGRFSG T G C+G
Sbjct: 430 RREYKEGEVIVIRYEGPRGGPGMREMLATTAALYGQGMGDKVALITDGRFSGATRGFCIG 489

Query: 501 HIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVLSK 560
           H+ PEA  GGPI LLR+GD I +D     L V    AE A R++ + P    + +G + K
Sbjct: 490 HVGPEAAVGGPIGLLRDGDVITIDATTGELSVALSDAELAERRKGWQPRRHDFQSGAIWK 549

Query: 561 YVKLVSSAAVGAV 573
           Y + V  A  GAV
Sbjct: 550 YAQTVGDAEKGAV 562


Lambda     K      H
   0.318    0.136    0.393 

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: 1012
Number of extensions: 44
Number of successful extensions: 4
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: 575
Length of database: 577
Length adjustment: 36
Effective length of query: 539
Effective length of database: 541
Effective search space:   291599
Effective search space used:   291599
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_012566366.1 RC1_RS05545 (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.3697884.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-212  691.1   0.8   5.8e-212  690.9   0.8    1.0  1  NCBI__GCF_000016185.1:WP_012566366.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016185.1:WP_012566366.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  690.9   0.8  5.8e-212  5.8e-212       1     541 [.      27     563 ..      27     565 .. 0.99

  Alignments for each domain:
  == domain 1  score: 690.9 bits;  conditional E-value: 5.8e-212
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++r+ ++a+G++++++ +P+++v+ +++e +P+++ l+  a++vk +++a  g++ ef ti+v+DGiamgh+G
  NCBI__GCF_000016185.1:WP_012566366.1  27 PHRSYYYAMGMTEQEIARPFVGVATCWNEAAPCNIALNRQAQAVKTGVKAEQGTPREFTTITVTDGIAMGHQG 99 
                                           689********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           mk sL+sre+iaDsve  +++h++Dalv ++ CDk +PGm+ma++rln+P+++++GG++ +gk++ ++++++ 
  NCBI__GCF_000016185.1:WP_012566366.1 100 MKASLVSREVIADSVELTMRGHCYDALVGLAGCDKSLPGMMMAMVRLNVPSVFMYGGSILPGKFR-GKDVTVQ 171
                                           *****************************************************************.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           dvfeavg+ +ag+++e++l+e+e +acP++g+C+G +tan+mac++ea+Gl+lPgs+ ++a  + + + a+ s
  NCBI__GCF_000016185.1:WP_012566366.1 172 DVFEAVGAFSAGRMDEKDLHELECCACPGSGACGGQYTANTMACVSEAIGLALPGSAGAPAPYESRDAYAEAS 244
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g+ +++lv+ n++Prdi+t++a+ena +++ a GGstn+ Lhl+aia+eag++++l+d+  + r++P +a+lk
  NCBI__GCF_000016185.1:WP_012566366.1 245 GRAVMKLVEMNLRPRDIVTRKALENAAVVVAASGGSTNAALHLPAIAHEAGIEFDLHDVAAVFRRTPYIADLK 317
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365
                                           P+g+ v +dl ++GGv+ ++k l   g lh d++tvtG+t+ae+l++v    +dq+vir+++ p++ +gg+  
  NCBI__GCF_000016185.1:WP_012566366.1 318 PGGRFVAKDLFEVGGVPVLMKALLDGGFLHGDCITVTGRTIAENLADVVFP-TDQEVIRPTSAPLSPTGGVVG 389
                                           ***********************************************9876.9******************** PP

                             TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                           L+Gnla++Ga+vk+ag+++  l+f Gpa+ f+ ee+a +a+ +++ keG+v+viryeGP+GgPGmremLa t+
  NCBI__GCF_000016185.1:WP_012566366.1 390 LRGNLAPQGAIVKVAGMKN--LRFSGPARCFDREEDAFAAVERREYKEGEVIVIRYEGPRGGPGMREMLATTA 460
                                           *******************..**************************************************** PP

                             TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                           al g G+g+kvaLitDGrfsG+trG++iGhv Peaa+gG+i+l++dGD i+iD++  +l +++s++elaerr+
  NCBI__GCF_000016185.1:WP_012566366.1 461 ALYGQGMGDKVALITDGRFSGATRGFCIGHVGPEAAVGGPIGLLRDGDVITIDATTGELSVALSDAELAERRK 533
                                           ************************************************************************* PP

                             TIGR00110 512 kakkkearevkgaLakyaklvssadkGavl 541
                                            ++++++  ++ga+ kya+ v  a+kGav+
  NCBI__GCF_000016185.1:WP_012566366.1 534 GWQPRRHDFQSGAIWKYAQTVGDAEKGAVT 563
                                           ****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (577 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 25.78
//
[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 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