Alignments for a candidate for ilvD in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methylobacterium nodulans ORS 2060

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_015928511.1 MNOD_RS08820 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_000022085.1:WP_015928511.1
          Length = 609

 Score =  978 bits (2529), Expect = 0.0
 Identities = 488/609 (80%), Positives = 528/609 (86%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRSRTTTHGRNMAGARGLWRATGMKD+DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPTYRSRTTTHGRNMAGARGLWRATGMKDADFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEQAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGMLMA+LRLNIP VFVSGGPMEAGKVV+ G    LDLVDAMVAAADD++ D D
Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVVLGGARKKLDLVDAMVAAADDRVGDAD 180

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           +Q IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATH DR+RLFVEAGHLIV
Sbjct: 181 LQVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADRRRLFVEAGHLIV 240

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
           DLARRYYEQDD   LPR IAS  AFENAMTLDIAMGGSTNTVLH+LAAAHE  + F+M D
Sbjct: 241 DLARRYYEQDDDSVLPRAIASFAAFENAMTLDIAMGGSTNTVLHLLAAAHEAGVPFSMTD 300

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           ID LSRRVP L KVAPA  DVHMEDVHRAGGIM ILGELD+ GLL+    +VHAE+L  A
Sbjct: 301 IDRLSRRVPVLCKVAPAVPDVHMEDVHRAGGIMGILGELDRAGLLDTSVGSVHAESLAAA 360

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           ++RWD+ R++S TV  FYRAAPGG+PTQ AFSQEAR+D LD DR  GV+R  EH +++DG
Sbjct: 361 LERWDVRRSDSPTVHAFYRAAPGGVPTQTAFSQEARFDALDLDRAGGVVRDAEHAYARDG 420

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVL GNLA DGCIVKTAGVD SIL F+GPA VFESQDA+V  IL+  VKAG+VV+IRY
Sbjct: 421 GLAVLYGNLATDGCIVKTAGVDASILAFAGPAHVFESQDAAVDGILSGRVKAGEVVLIRY 480

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGP+GGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGG+SGLSIGH SPEAA GG IGL
Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGLIGL 540

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
           V +GD I+IDIPNR I L V E EL  RRA Q+A+GW P   RKR V+ AL+AYA   TS
Sbjct: 541 VEQGDRIEIDIPNRRIHLAVDEAELERRRAAQEARGWQPAVPRKRKVSAALRAYAMLTTS 600

Query: 601 ADRGAVRDL 609
           A +GAVR L
Sbjct: 601 AAQGAVRKL 609


Lambda     K      H
   0.318    0.134    0.391 

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: 1307
Number of extensions: 45
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: 612
Length of database: 609
Length adjustment: 37
Effective length of query: 575
Effective length of database: 572
Effective search space:   328900
Effective search space used:   328900
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_015928511.1 MNOD_RS08820 (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.15700.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-251  821.3   1.5     2e-251  821.1   1.5    1.0  1  lcl|NCBI__GCF_000022085.1:WP_015928511.1  MNOD_RS08820 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015928511.1  MNOD_RS08820 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  821.1   1.5    2e-251    2e-251       2     542 ..      18     608 ..      17     609 .] 0.99

  Alignments for each domain:
  == domain 1  score: 821.1 bits;  conditional E-value: 2e-251
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar l++atG+kd+d++kPiiavvns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg
  lcl|NCBI__GCF_000022085.1:WP_015928511.1  18 ARGLWRATGMKDADFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEQAGGVAKEFNTIAVDDGIAMG 86 
                                               689****************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniPa++vsGGpmeagk+ l
  lcl|NCBI__GCF_000022085.1:WP_015928511.1  87 HDGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVVL 155
                                               ********************************************************************* PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               +   +++d+++a++++a++++ +++l+ iersacPt+gsCsG+ftansm+cltealGlslPg++++lat
  lcl|NCBI__GCF_000022085.1:WP_015928511.1 156 GGARKKLDLVDAMVAAADDRVGDADLQVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLAT 224
                                               ********************************************************************* PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +a++++l+ ++g+ iv+l +++++       Pr i++ +afena+tld+a+GGstntvLhlla+a+eag
  lcl|NCBI__GCF_000022085.1:WP_015928511.1 225 HADRRRLFVEAGHLIVDLARRYYEqdddsvlPRAIASFAAFENAMTLDIAMGGSTNTVLHLLAAAHEAG 293
                                               ********************************************************************* PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338
                                               v +s+ d+drlsr+vP+l+k++P+   v +ed+hraGG++++l+eld++gll++ + +v  ++la  le
  lcl|NCBI__GCF_000022085.1:WP_015928511.1 294 VPFSMTDIDRLSRRVPVLCKVAPAVPDVhMEDVHRAGGIMGILGELDRAGLLDTSVGSVHAESLAAALE 362
                                               ************************98888**************************************** PP

                                 TIGR00110 339 kvkvlr.................................vdqd....virsldnpvkkegglavLkGnl 370
                                               + +v+r                                 +  d    v+r  ++++ ++gglavL+Gnl
  lcl|NCBI__GCF_000022085.1:WP_015928511.1 363 RWDVRRsdsptvhafyraapggvptqtafsqearfdaldL--DraggVVRDAEHAYARDGGLAVLYGNL 429
                                               **********************************999663..33467********************** PP

                                 TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439
                                               a++G++vk+agv+ +il f Gpa+vfes+++a+++il+g+vk+G+vv+iryeGP+GgPGm+emL+Pts+
  lcl|NCBI__GCF_000022085.1:WP_015928511.1 430 ATDGCIVKTAGVDASILAFAGPAHVFESQDAAVDGILSGRVKAGEVVLIRYEGPRGGPGMQEMLYPTSY 498
                                               ********************************************************************* PP

                                 TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508
                                               l++ GLgk++aL+tDGrfsGg++GlsiGhvsPeaaegG i+lve+GD+i+iDi+nr+++l+v+e+el++
  lcl|NCBI__GCF_000022085.1:WP_015928511.1 499 LKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGLIGLVEQGDRIEIDIPNRRIHLAVDEAELER 567
                                               ********************************************************************* PP

                                 TIGR00110 509 rrakakkkea.......revkgaLakyaklvssadkGavld 542
                                               rra+++++++       r+v+ aL++ya l +sa +Gav++
  lcl|NCBI__GCF_000022085.1:WP_015928511.1 568 RRAAQEARGWqpavprkRKVSAALRAYAMLTTSAAQGAVRK 608
                                               *********99****9999********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (609 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: 00:00:00.03
# Mc/sec: 10.12
//
[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