Alignments for a candidate for ilvD in Frankia alni ACN14A

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Frankia alni ACN14A

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_041941157.1 FRAAL_RS29895 dihydroxy-acid dehydratase

Query= BRENDA::Q8NQZ9
         (613 letters)



>NCBI__GCF_000058485.1:WP_041941157.1
          Length = 617

 Score =  863 bits (2231), Expect = 0.0
 Identities = 427/613 (69%), Positives = 504/613 (82%), Gaps = 2/613 (0%)

Query: 1   MIPLRSKVTTVGRNAAGARALWRATGTKENEFGKPIVAIVNSYTQFVPGHVHLKNVGDIV 60
           M  LRS+ TT GRN AGARALWRATG  +++FGKPI+AI NS+TQFVPGHVHL+N+G +V
Sbjct: 1   MPALRSRTTTHGRNMAGARALWRATGMTDDDFGKPIIAIANSFTQFVPGHVHLRNLGALV 60

Query: 61  ADAVRKAGGVPKEFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAHTADAMVCIS 120
           A+AV ++GGV +EFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAH ADA+VCIS
Sbjct: 61  AEAVAESGGVGREFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLNAAMRLNIPVVFVSGGPMEAGKAVVVDGVAHAPTDLITAISASASDAVDD 180
           NCDKITPGML AA+RLNIP VFVSGG ME+G AV+  G A +  DLITA+SA+ +  V D
Sbjct: 121 NCDKITPGMLLAALRLNIPTVFVSGGAMESGNAVISGGTARSKLDLITAMSAAVNPEVSD 180

Query: 181 AGLAAVEASACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAARRALFEKAGET 240
             L+ +E SACPTCGSCSGMFTANSMNCLTEA+GLSLPGNGSTLAT AARR LF +AG  
Sbjct: 181 GDLSTIERSACPTCGSCSGMFTANSMNCLTEAMGLSLPGNGSTLATAAARRELFVEAGRL 240

Query: 241 VVELCRRYYGEEDESVLPRGIATKKAFENAMALDMAMGGSTNTILHILAAAQEGEVDFDL 300
           VV+L RRYY ++DE+VLPR IAT  AF NA A+D+AMGGSTNT+LH+LAAA E  VD  L
Sbjct: 241 VVDLARRYYEKDDEAVLPRSIATAAAFRNAFAVDVAMGGSTNTVLHLLAAAVEAGVDVTL 300

Query: 301 ADIDELSKNVPCLSKVAPNS-DYHMEDVHRAGGIPALLGELNRGGLLNKDVHSVHSNDLE 359
           ADID++S+ VPCL KVAP+S  Y+MEDVHRAGGIPA+LGEL+R GLL+++ HSVH+  L 
Sbjct: 301 ADIDQISRTVPCLCKVAPSSTHYYMEDVHRAGGIPAILGELDRAGLLDRNTHSVHAASLR 360

Query: 360 GWLDDWDIRSGKTTEVATELFHAAPGGIRTTEAFSTENRWDELDTDAAKGCIRDVEHAYT 419
            +LD WD+R  + +  A ELFHAAPGG+RT E FS+ NRWD LDTDA  GCIR VEHAY+
Sbjct: 361 EFLDRWDVRGAQPSPDAVELFHAAPGGVRTIEPFSSTNRWDSLDTDAENGCIRSVEHAYS 420

Query: 420 ADGGLVVLRGNISPDGAVIKSAGIEEELWNFTGPARVVESQEEAVSVILTKTIQAGEVLV 479
           A+GGL VL GN++ DGAV+K+AG++E  W+F GPA VVESQE+AV  IL K +Q G+V++
Sbjct: 421 AEGGLAVLFGNLATDGAVVKTAGVDESQWSFRGPALVVESQEDAVDAILNKRVQPGDVII 480

Query: 480 VRYEGPSGGPGMQEMLHPTAFLKGSGLGKKCALITDGRFSGGSSGLSIGHVSPEAAHGGV 539
           VRYEGP GGPGMQEML+PTAFLKG GLG KCALITDGRFSGGSSGLSIGHVSPEAAHGG 
Sbjct: 481 VRYEGPRGGPGMQEMLYPTAFLKGRGLGPKCALITDGRFSGGSSGLSIGHVSPEAAHGGT 540

Query: 540 IGLIENGDIVSIDVHNRKLEVQVSDEELQRRRDAMNASEKPWQPVNRNRVVTKALRAYAK 599
           I L+ +GD++ ID+  R+LE+ VSDEEL RRR  + A+   ++P NR R V+ ALRAYA 
Sbjct: 541 IALVRDGDVIDIDIPTRRLELLVSDEELARRRAELEAA-GGYRPANRERAVSAALRAYAA 599

Query: 600 MATSADKGAVRQV 612
           MATSA  GA R V
Sbjct: 600 MATSASTGAARDV 612


Lambda     K      H
   0.315    0.132    0.385 

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: 1153
Number of extensions: 32
Number of successful extensions: 3
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: 613
Length of database: 617
Length adjustment: 37
Effective length of query: 576
Effective length of database: 580
Effective search space:   334080
Effective search space used:   334080
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_041941157.1 FRAAL_RS29895 (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.17638.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-244  796.3   0.7   8.1e-244  796.1   0.7    1.0  1  lcl|NCBI__GCF_000058485.1:WP_041941157.1  FRAAL_RS29895 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_041941157.1  FRAAL_RS29895 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  796.1   0.7  8.1e-244  8.1e-244       2     542 ..      18     611 ..      17     612 .. 0.98

  Alignments for each domain:
  == domain 1  score: 796.1 bits;  conditional E-value: 8.1e-244
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG++d+d++kPiia++ns+t++vPghvhl++l+ lv+e++ ++Ggv  efntiav+DGiamg
  lcl|NCBI__GCF_000058485.1:WP_041941157.1  18 ARALWRATGMTDDDFGKPIIAIANSFTQFVPGHVHLRNLGALVAEAVAESGGVGREFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsreiiaDsve++v+ah++Dalv+is+CDki+PGml+aalrlniP+++vsGG+me+g+  +
  lcl|NCBI__GCF_000058485.1:WP_041941157.1  87 HGGMLYSLPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLLAALRLNIPTVFVSGGAMESGNAVI 155
                                               *****************************************************************9877 PP

                                 TIGR00110 140 ..sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206
                                                 +   +++d++ a+ ++ ++++s+ +l++iersacPt+gsCsG+ftansm+cltea+GlslPg++++l
  lcl|NCBI__GCF_000058485.1:WP_041941157.1 156 sgGTARSKLDLITAMSAAVNPEVSDGDLSTIERSACPTCGSCSGMFTANSMNCLTEAMGLSLPGNGSTL 224
                                               44778899************************************************************* PP

                                 TIGR00110 207 atsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiake 268
                                               at a ++el+ ++g+ +v+l +++++       Pr+i+t +af na+++d+a+GGstntvLhlla+a e
  lcl|NCBI__GCF_000058485.1:WP_041941157.1 225 ATAAARRELFVEAGRLVVDLARRYYEkddeavlPRSIATAAAFRNAFAVDVAMGGSTNTVLHLLAAAVE 293
                                               ********************************************************************* PP

                                 TIGR00110 269 agvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaet 336
                                               agv+++l d+d++sr+vP+l+k++Ps+ ++ +ed+hraGG++a+l+eld++gll++++++v   +l e 
  lcl|NCBI__GCF_000058485.1:WP_041941157.1 294 AGVDVTLADIDQISRTVPCLCKVAPSSTHYyMEDVHRAGGIPAILGELDRAGLLDRNTHSVHAASLREF 362
                                               *************************998877************************************** PP

                                 TIGR00110 337 lekvkvlr....................................vdqdvirsldnpvkkegglavLkGn 369
                                               l++ +v+                                     +++ +irs+++++++egglavL+Gn
  lcl|NCBI__GCF_000058485.1:WP_041941157.1 363 LDRWDVRGaqpspdavelfhaapggvrtiepfsstnrwdsldtdAENGCIRSVEHAYSAEGGLAVLFGN 431
                                               ******9999******************************88766667********************* PP

                                 TIGR00110 370 laeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                               la++Gavvk+agv+e+ + f+Gpa v es+e+a++ail+++v+ Gdv+++ryeGP+GgPGm+emL+Pt+
  lcl|NCBI__GCF_000058485.1:WP_041941157.1 432 LATDGAVVKTAGVDESQWSFRGPALVVESQEDAVDAILNKRVQPGDVIIVRYEGPRGGPGMQEMLYPTA 500
                                               ********************************************************************* PP

                                 TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeela 507
                                               +l+g GLg k+aLitDGrfsGg++GlsiGhvsPeaa+gG+ialv+dGD i iDi+ r+l+l vs+eela
  lcl|NCBI__GCF_000058485.1:WP_041941157.1 501 FLKGRGLGPKCALITDGRFSGGSSGLSIGHVSPEAAHGGTIALVRDGDVIDIDIPTRRLELLVSDEELA 569
                                               ********************************************************************* PP

                                 TIGR00110 508 errakakkkea.......revkgaLakyaklvssadkGavld 542
                                               +rra+ ++ +        r v+ aL++ya +++sa++Ga++d
  lcl|NCBI__GCF_000058485.1:WP_041941157.1 570 RRRAELEAAGGyrpanreRAVSAALRAYAAMATSASTGAARD 611
                                               *****999887788899999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (617 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.32
//
[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