Alignments for a candidate for ilvD in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Saccharomonospora cyanea NA-134

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_005454216.1 SACCYDRAFT_RS05065 dihydroxy-acid dehydratase

Query= BRENDA::Q8NQZ9
         (613 letters)



>NCBI__GCF_000244975.1:WP_005454216.1
          Length = 614

 Score = 1004 bits (2597), Expect = 0.0
 Identities = 492/613 (80%), Positives = 544/613 (88%)

Query: 1   MIPLRSKVTTVGRNAAGARALWRATGTKENEFGKPIVAIVNSYTQFVPGHVHLKNVGDIV 60
           M  LRS+ TT GRNAAGAR+LWRATG  +++FGKPIVAI NSYTQFVPGHVHLK++G++V
Sbjct: 1   MPALRSRTTTHGRNAAGARSLWRATGMTDSDFGKPIVAIANSYTQFVPGHVHLKDLGEVV 60

Query: 61  ADAVRKAGGVPKEFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAHTADAMVCIS 120
           A+AVR+AGGVP+EF+TIAVDDGIAMGH GMLYSLPSREIIADSVEYM NAH ADA+VCIS
Sbjct: 61  AEAVREAGGVPREFHTIAVDDGIAMGHSGMLYSLPSREIIADSVEYMANAHQADALVCIS 120

Query: 121 NCDKITPGMLNAAMRLNIPVVFVSGGPMEAGKAVVVDGVAHAPTDLITAISASASDAVDD 180
           NCDKITPGMLNAAMRLNIP VFVSGGPMEAGKAVVVDGVAHAPTDLITAI+ASA+ AVDD
Sbjct: 121 NCDKITPGMLNAAMRLNIPTVFVSGGPMEAGKAVVVDGVAHAPTDLITAIAASANSAVDD 180

Query: 181 AGLAAVEASACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAARRALFEKAGET 240
           AGL+ VE SACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAARR LF +AG T
Sbjct: 181 AGLSVVEQSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAARRELFTEAGRT 240

Query: 241 VVELCRRYYGEEDESVLPRGIATKKAFENAMALDMAMGGSTNTILHILAAAQEGEVDFDL 300
           VVEL +R+YGE+DES LPR IATK+AFENAMALDMAMGGSTNT+LHILAAA+EGE+DF L
Sbjct: 241 VVELAKRWYGEDDESALPRSIATKQAFENAMALDMAMGGSTNTVLHILAAAREGEIDFTL 300

Query: 301 ADIDELSKNVPCLSKVAPNSDYHMEDVHRAGGIPALLGELNRGGLLNKDVHSVHSNDLEG 360
            DID + + VPCLSKV+PNSDYHMEDVHRAGGIPA+LGEL+RGG LN DVHSVHS+ LE 
Sbjct: 301 DDIDRIGREVPCLSKVSPNSDYHMEDVHRAGGIPAILGELHRGGFLNTDVHSVHSSSLEE 360

Query: 361 WLDDWDIRSGKTTEVATELFHAAPGGIRTTEAFSTENRWDELDTDAAKGCIRDVEHAYTA 420
           WL  WDIR G  +E A ELFHAAPGG+RTTEAFST NRW  LDTDAA GC+RDVEHAYTA
Sbjct: 361 WLSTWDIRGGSPSERALELFHAAPGGVRTTEAFSTSNRWSSLDTDAANGCVRDVEHAYTA 420

Query: 421 DGGLVVLRGNISPDGAVIKSAGIEEELWNFTGPARVVESQEEAVSVILTKTIQAGEVLVV 480
            GGL VLRGN++ +GAVIKSAGI+EELW F GPARVVESQEEAVS IL K +++GEV+VV
Sbjct: 421 SGGLTVLRGNLAENGAVIKSAGIDEELWRFRGPARVVESQEEAVSAILNKEVRSGEVIVV 480

Query: 481 RYEGPSGGPGMQEMLHPTAFLKGSGLGKKCALITDGRFSGGSSGLSIGHVSPEAAHGGVI 540
           RYEGP+GGPGMQEMLHPTAFLKG+GLGK CALITDGRFSGGSSG+S+GH+SPEAA GG I
Sbjct: 481 RYEGPAGGPGMQEMLHPTAFLKGAGLGKVCALITDGRFSGGSSGISVGHISPEAAAGGTI 540

Query: 541 GLIENGDIVSIDVHNRKLEVQVSDEELQRRRDAMNASEKPWQPVNRNRVVTKALRAYAKM 600
           GL+ENGD + IDVH RKLE+ V  E L  RR  M ASE+PWQPVNR R VT ALRAYA+M
Sbjct: 541 GLVENGDEILIDVHERKLELLVDAEVLAERRAKMEASERPWQPVNRQRPVTAALRAYARM 600

Query: 601 ATSADKGAVRQVD 613
           ATSAD GAVR  D
Sbjct: 601 ATSADTGAVRDPD 613


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: 1253
Number of extensions: 44
Number of successful extensions: 1
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: 614
Length adjustment: 37
Effective length of query: 576
Effective length of database: 577
Effective search space:   332352
Effective search space used:   332352
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_005454216.1 SACCYDRAFT_RS05065 (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.13722.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-240  783.8   1.1   4.9e-240  783.6   1.1    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454216.1  SACCYDRAFT_RS05065 dihydroxy-aci


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454216.1  SACCYDRAFT_RS05065 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  783.6   1.1  4.9e-240  4.9e-240       2     542 ..      18     611 ..      17     612 .. 0.98

  Alignments for each domain:
  == domain 1  score: 783.6 bits;  conditional E-value: 4.9e-240
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar+l++atG++d d++kPi+a++nsyt++vPghvhlkdl+++v+e++++aGgv+ ef tiav+DGiamg
  lcl|NCBI__GCF_000244975.1:WP_005454216.1  18 ARSLWRATGMTDSDFGKPIVAIANSYTQFVPGHVHLKDLGEVVAEAVREAGGVPREFHTIAVDDGIAMG 86 
                                               69******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsreiiaDsve++++ah++Dalv+is+CDki+PGml aa+rlniP+++vsGGpmeagk  +
  lcl|NCBI__GCF_000244975.1:WP_005454216.1  87 HSGMLYSLPSREIIADSVEYMANAHQADALVCISNCDKITPGMLNAAMRLNIPTVFVSGGPMEAGKAVV 155
                                               *******************************************************************99 PP

                                 TIGR00110 140 sekidl..vdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206
                                                + +    +d++ a+ + a++ ++++ l+ +e+sacPt+gsCsG+ftansm+cltealGlslPg++++l
  lcl|NCBI__GCF_000244975.1:WP_005454216.1 156 VDGVAHapTDLITAIAASANSAVDDAGLSVVEQSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTL 224
                                               7776542279*********************************************************** PP

                                 TIGR00110 207 atsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiake 268
                                               at+a ++el++++g+++vel k+ +        Pr+i+tk+afena++ld+a+GGstntvLh+la+a+e
  lcl|NCBI__GCF_000244975.1:WP_005454216.1 225 ATHAARRELFTEAGRTVVELAKRWYGeddesalPRSIATKQAFENAMALDMAMGGSTNTVLHILAAARE 293
                                               ***********************998899999************************************* PP

                                 TIGR00110 269 agvklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetl 337
                                                +++++ldd+dr+ r+vP+l+k++P++++ +ed+hraGG++a+l+el++ g l++d+++v  ++l+e l
  lcl|NCBI__GCF_000244975.1:WP_005454216.1 294 GEIDFTLDDIDRIGREVPCLSKVSPNSDYHMEDVHRAGGIPAILGELHRGGFLNTDVHSVHSSSLEEWL 362
                                               ********************************************************************* PP

                                 TIGR00110 338 ekvkvlr....................................vdqdvirsldnpvkkegglavLkGnl 370
                                               ++ +++                                     + + ++r +++++++ ggl vL+Gnl
  lcl|NCBI__GCF_000244975.1:WP_005454216.1 363 STWDIRGgspseralelfhaapggvrtteafstsnrwssldtdAANGCVRDVEHAYTASGGLTVLRGNL 431
                                               ****99999******************************77655556********************** PP

                                 TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439
                                               ae+Gav+k ag++e++++f+Gpa+v es+eea+ ail+++v+ G+v+v+ryeGP GgPGm+emL+Pt++
  lcl|NCBI__GCF_000244975.1:WP_005454216.1 432 AENGAVIKSAGIDEELWRFRGPARVVESQEEAVSAILNKEVRSGEVIVVRYEGPAGGPGMQEMLHPTAF 500
                                               ********************************************************************* PP

                                 TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508
                                               l+g+GLgk +aLitDGrfsGg++G+s+Gh+sPeaa+gG+i+lve+GD+i iD+++rkl+l v+ e lae
  lcl|NCBI__GCF_000244975.1:WP_005454216.1 501 LKGAGLGKVCALITDGRFSGGSSGISVGHISPEAAAGGTIGLVENGDEILIDVHERKLELLVDAEVLAE 569
                                               ********************************************************************* PP

                                 TIGR00110 509 rrakakkkea........revkgaLakyaklvssadkGavld 542
                                               rrak+++ e         r v  aL++ya++++sad+Gav+d
  lcl|NCBI__GCF_000244975.1:WP_005454216.1 570 RRAKMEASERpwqpvnrqRPVTAALRAYARMATSADTGAVRD 611
                                               ****9998888899*999999*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (614 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: 00:00:00.04
# Mc/sec: 7.78
//
[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