Alignments for a candidate for ilvD in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Hydrogenovibrio marinus DSM 11271

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_029908057.1 P166_RS0101445 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_000711315.1:WP_029908057.1
          Length = 617

 Score =  917 bits (2371), Expect = 0.0
 Identities = 445/612 (72%), Positives = 519/612 (84%), Gaps = 3/612 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRS+T+THGRNMAGAR LWRATGM+  DFGKPIIA+ NSFTQFVPGHVHLKD+GQLV
Sbjct: 1   MPAYRSKTSTHGRNMAGARALWRATGMQTEDFGKPIIAIANSFTQFVPGHVHLKDMGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AR IE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR+LIADSVEYM NAHCADA+VCIS
Sbjct: 61  ARVIEGAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMCNAHCADALVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGM+MA++RLNIPT+FV+GGPME+GK V+ G+   LDLVDAMV AAD   SD D
Sbjct: 121 NCDKITPGMMMAAMRLNIPTIFVTGGPMESGKTVLGGEGIKLDLVDAMVMAADSHCSDSD 180

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           V+ +ERSACPTCGSCSGMFTANSMNCL EALG++LPGNG+TLATH DR+ LF EAG  IV
Sbjct: 181 VEEVERSACPTCGSCSGMFTANSMNCLAEALGIALPGNGTTLATHADRRHLFEEAGRRIV 240

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
           +LA++YYEQDD   LPR+IA+++AFENAM LD+AMGGSTNTVLH+LA A E E++FTMAD
Sbjct: 241 ELAKQYYEQDDASVLPRSIATREAFENAMALDVAMGGSTNTVLHLLAIAREAEVNFTMAD 300

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           +D +SRRVPCL KVAP     HMEDVHRAGGIM ILGEL++GGL+N D  TVHA T+G A
Sbjct: 301 MDHISRRVPCLVKVAPNSKIFHMEDVHRAGGIMRILGELERGGLINTDVKTVHASTMGAA 360

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           ++ WDITRT+ E V  FYRAAPG + T  AFSQ  RW E+D D E G +RS+EH ++++G
Sbjct: 361 LELWDITRTDDEAVTTFYRAAPGNVRTTEAFSQNKRWKEVDDDDEKGCVRSLEHAYTQEG 420

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVL GN+A+DGCIVKTAGVDE I KFSGPA+++ESQ+ +V AIL +EVKAGDVVVIRY
Sbjct: 421 GLAVLYGNIALDGCIVKTAGVDEEIFKFSGPAKIYESQEDAVAAILGDEVKAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGP+GGPGMQEMLYPTSYLKSKGLGK+CAL+TDGRFSGGTSGLSIGH SPEAA GG IGL
Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKSCALLTDGRFSGGTSGLSIGHCSPEAAEGGNIGL 540

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597
           +  GD+I+IDIPNR+I +++++ ELA RR    AKG   W P + R R V+ AL+AYAA 
Sbjct: 541 IESGDIIEIDIPNRSIQVKLTDEELAERRQAMVAKGKLAWKPMKERPRKVSAALRAYAAM 600

Query: 598 ATSADRGAVRDL 609
            TSA  GAVR++
Sbjct: 601 TTSAAFGAVRNV 612


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: 1220
Number of extensions: 42
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: 612
Length of database: 617
Length adjustment: 37
Effective length of query: 575
Effective length of database: 580
Effective search space:   333500
Effective search space used:   333500
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_029908057.1 P166_RS0101445 (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.506799.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-254  830.2   6.3   4.5e-254  829.9   6.3    1.0  1  NCBI__GCF_000711315.1:WP_029908057.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711315.1:WP_029908057.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  829.9   6.3  4.5e-254  4.5e-254       2     542 ..      18     611 ..      17     612 .. 0.99

  Alignments for each domain:
  == domain 1  score: 829.9 bits;  conditional E-value: 4.5e-254
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           aral++atG++ ed++kPiia++ns+t++vPghvhlkd+++lv++ ie aGgvakefntiav+DGiamgh+Gm
  NCBI__GCF_000711315.1:WP_029908057.1  18 ARALWRATGMQTEDFGKPIIAIANSFTQFVPGHVHLKDMGQLVARVIEGAGGVAKEFNTIAVDDGIAMGHDGM 90 
                                           79*********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysLpsr++iaDsve++++ah++Dalv+is+CDki+PGm+maa+rlniP+i+v+GGpme+gkt l+ + +++d
  NCBI__GCF_000711315.1:WP_029908057.1  91 LYSLPSRDLIADSVEYMCNAHCADALVCISNCDKITPGMMMAAMRLNIPTIFVTGGPMESGKTVLGGEGIKLD 163
                                           ************************************************************************* PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                           +++a++++a+++ s++++ee+ersacPt+gsCsG+ftansm+cl+ealG++lPg++t+lat+a++++l++++g
  NCBI__GCF_000711315.1:WP_029908057.1 164 LVDAMVMAADSHCSDSDVEEVERSACPTCGSCSGMFTANSMNCLAEALGIALPGNGTTLATHADRRHLFEEAG 236
                                           ************************************************************************* PP

                             TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286
                                           +rivel k++++       Pr+i+t+eafena++ld+a+GGstntvLhllaia+ea+v++++ d+d++sr+vP
  NCBI__GCF_000711315.1:WP_029908057.1 237 RRIVELAKQYYEqddasvlPRSIATREAFENAMALDVAMGGSTNTVLHLLAIAREAEVNFTMADMDHISRRVP 309
                                           ************************************************************************* PP

                             TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344
                                           +l+k++P++k + +ed+hraGG++ +l+el++ gl+++d++tv  +t++  le  +++r              
  NCBI__GCF_000711315.1:WP_029908057.1 310 CLVKVAPNSKIFhMEDVHRAGGIMRILGELERGGLINTDVKTVHASTMGAALELWDITRtddeavttfyraap 382
                                           ***********99********************************************999************* PP

                             TIGR00110 345 ...................vdqd....virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpak 394
                                                                 d    ++rsl++++++egglavL+Gn+a +G++vk+agv+e+i kf Gpak
  NCBI__GCF_000711315.1:WP_029908057.1 383 gnvrtteafsqnkrwkevdD--DdekgCVRSLEHAYTQEGGLAVLYGNIALDGCIVKTAGVDEEIFKFSGPAK 453
                                           ****************9751..33567********************************************** PP

                             TIGR00110 395 vfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiG 467
                                           ++es+e+a++ailg +vk+GdvvviryeGP+GgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiG
  NCBI__GCF_000711315.1:WP_029908057.1 454 IYESQEDAVAAILGDEVKAGDVVVIRYEGPRGGPGMQEMLYPTSYLKSKGLGKSCALLTDGRFSGGTSGLSIG 526
                                           ************************************************************************* PP

                             TIGR00110 468 hvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea..........revkgaLakyak 530
                                           h sPeaaegG+i+l+e GD+i+iDi+nr +++++ +eelaerr+++++k++          r+v+ aL++ya 
  NCBI__GCF_000711315.1:WP_029908057.1 527 HCSPEAAEGGNIGLIESGDIIEIDIPNRSIQVKLTDEELAERRQAMVAKGKlawkpmkerpRKVSAALRAYAA 599
                                           *************************************************9999******************** PP

                             TIGR00110 531 lvssadkGavld 542
                                           + +sa  Gav++
  NCBI__GCF_000711315.1:WP_029908057.1 600 MTTSAAFGAVRN 611
                                           **********86 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 21.60
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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