GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Azohydromonas australica DSM 1124

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_028999050.1 H537_RS0118680 dihydroxy-acid dehydratase

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



>NCBI__GCF_000430725.1:WP_028999050.1
          Length = 559

 Score =  877 bits (2267), Expect = 0.0
 Identities = 425/557 (76%), Positives = 497/557 (89%), Gaps = 1/557 (0%)

Query: 1   MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60
           M+ N+RS+NIT+GVAR+PNRSMYYA+GY + DF KPM+G+ANGHSTITPCN+GLQRLADA
Sbjct: 1   MSDNRRSRNITEGVARAPNRSMYYAMGYTEGDFGKPMIGVANGHSTITPCNSGLQRLADA 60

Query: 61  AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120
           A++ ++A+ ANPQ+FGTPTISDGM+MGTEGMKYSL+SREVI+DC+ET   GQWMDGV+VI
Sbjct: 61  AVEGLQAAGANPQIFGTPTISDGMAMGTEGMKYSLVSREVISDCVETCVGGQWMDGVLVI 120

Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180
           GGCDKNMPGGM+ + R NVP IYVYGGTI PG +KG+DL IVS FEAVG+F+AG+MS+ED
Sbjct: 121 GGCDKNMPGGMMGMLRANVPAIYVYGGTILPGRYKGQDLNIVSVFEAVGQFSAGKMSEED 180

Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240
           F  +EK A P +GSCGGMYTANTMSS+FEALGMSL YSST AN   EKV+S   +A VLV
Sbjct: 181 FCEIEKRAIPGSGSCGGMYTANTMSSAFEALGMSLPYSSTEANVHDEKVESTRRAAAVLV 240

Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300
           EA+K+D+KPRDI+T++SIENAVA+IMATGGSTNAVLH+LAIAHAAEVEWTIDDFER+R+K
Sbjct: 241 EAVKKDLKPRDIVTKQSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWTIDDFERMRKK 300

Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360
           V V+CNLKPSGQY+A DLH+AGGIP VMK LLKAG+L+GDC+TITG+T+AE L +VPD  
Sbjct: 301 VAVLCNLKPSGQYLAVDLHRAGGIPAVMKELLKAGLLNGDCMTITGKTVAENLADVPDL- 359

Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420
            A+QDVI P+   LYA+GHLAILKGNL+ EG VAKITGLKNPVITGPARVF+DEQSA+ A
Sbjct: 360 TAEQDVIRPVSDPLYAQGHLAILKGNLSPEGCVAKITGLKNPVITGPARVFDDEQSALAA 419

Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480
           I+A +I AGD++VLRYLGPKGGPGMPEMLAPT A+IG+GLGESVG ITDGRFSGGTWGMV
Sbjct: 420 IMAGQIKAGDVMVLRYLGPKGGPGMPEMLAPTGALIGQGLGESVGLITDGRFSGGTWGMV 479

Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540
           VGHVAPEAY GG IALVQEGD+ITIDAH+LLLQLNV + E+ARRRA WKQPAPRYTRGVL
Sbjct: 480 VGHVAPEAYDGGNIALVQEGDAITIDAHQLLLQLNVDEAEIARRRAQWKQPAPRYTRGVL 539

Query: 541 AKFSKLASTASKGAVTD 557
           AKF++ A +AS GAV D
Sbjct: 540 AKFARNACSASSGAVLD 556


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: 1109
Number of extensions: 43
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: 559
Length adjustment: 36
Effective length of query: 521
Effective length of database: 523
Effective search space:   272483
Effective search space used:   272483
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_028999050.1 H537_RS0118680 (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.3023975.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-230  751.5   5.7   2.9e-230  751.3   5.7    1.0  1  NCBI__GCF_000430725.1:WP_028999050.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_028999050.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  751.3   5.7  2.9e-230  2.9e-230       1     542 [.      18     556 ..      18     557 .. 1.00

  Alignments for each domain:
  == domain 1  score: 751.3 bits;  conditional E-value: 2.9e-230
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++r++++a+G+++ d++kP+i+v+n++++i+P++  l+ la+++ e+++aaG+ ++ f+t ++sDG+amg+eG
  NCBI__GCF_000430725.1:WP_028999050.1  18 PNRSMYYAMGYTEGDFGKPMIGVANGHSTITPCNSGLQRLADAAVEGLQAAGANPQIFGTPTISDGMAMGTEG 90 
                                           68*********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           mkysL+sre+i+D vet v ++++D+++vi+ CDk++PG +m++lr n+Pai v+GG++ +g++k ++++++v
  NCBI__GCF_000430725.1:WP_028999050.1  91 MKYSLVSREVISDCVETCVGGQWMDGVLVIGGCDKNMPGGMMGMLRANVPAIYVYGGTILPGRYK-GQDLNIV 162
                                           *****************************************************************.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           +vfeavg+ +agk+see+  eie+ a P++gsC+G++tan+m++++ealG+slP+sst + ++ ek e+++++
  NCBI__GCF_000430725.1:WP_028999050.1 163 SVFEAVGQFSAGKMSEEDFCEIEKRAIPGSGSCGGMYTANTMSSAFEALGMSLPYSSTEANVHDEKVESTRRA 235
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           ++ +ve+vkk++kPrdi+tk+++ena+++++a+GGstn+vLh laia+ a+v+ ++ddf+r+++kv +l++lk
  NCBI__GCF_000430725.1:WP_028999050.1 236 AAVLVEAVKKDLKPRDIVTKQSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWTIDDFERMRKKVAVLCNLK 308
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365
                                           Psg+++ +dlhraGG++av+kel k+gll+ d++t+tGkt+ae+l++v+ l+++qdvir++++p++++g+la+
  NCBI__GCF_000430725.1:WP_028999050.1 309 PSGQYLAVDLHRAGGIPAVMKELLKAGLLNGDCMTITGKTVAENLADVPDLTAEQDVIRPVSDPLYAQGHLAI 381
                                           ************************************************************************* PP

                             TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                           LkGnl++eG+v+ki+g ++   +++Gpa+vf++e+ al+ai++g++k+Gdv+v+ry GPkGgPGm+emLaPt 
  NCBI__GCF_000430725.1:WP_028999050.1 382 LKGNLSPEGCVAKITGLKN--PVITGPARVFDDEQSALAAIMAGQIKAGDVMVLRYLGPKGGPGMPEMLAPTG 452
                                           *******************..999************************************************* PP

                             TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                           al+g GLg++v+LitDGrfsGgt G+++Ghv+Pea+ gG+ialv++GD i+iD+++  l+l+v+e+e+a+rra
  NCBI__GCF_000430725.1:WP_028999050.1 453 ALIGQGLGESVGLITDGRFSGGTWGMVVGHVAPEAYDGGNIALVQEGDAITIDAHQLLLQLNVDEAEIARRRA 525
                                           ************************************************************************* PP

                             TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542
                                           ++k++ +r+++g+Lak+a+ + sa++Gavld
  NCBI__GCF_000430725.1:WP_028999050.1 526 QWKQPAPRYTRGVLAKFARNACSASSGAVLD 556
                                           *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (559 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 27.50
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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